Methods for diagnosing colon cancer using MicroRNA signatures

ABSTRACT

The present invention provides novel methods and compositions for the diagnosis and treatment of solid cancers. The invention also provides methods of identifying inhibitors of tumorigenesis.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is filed under 35 U.S.C §111(a) as a divisional application which claims priority under 35 U.S.C. §119, 35 U.S.C. §120 and the Patent Cooperation Treaty to: parent application U.S. Ser. No. 12/160,061 filed under 35 U.S.C. §371 on Jul. 3, 2008, now allowed; which claims priority to PCT/US2007/000159 filed under the authority of the Patent Cooperation Treaty on Jan. 3, 2007, published; which claims priority to U.S. Provisional Application Ser. No. 60/756,585 filed under 35 U.S.C. §111(b) on Jan. 5, 2006; the disclosures of all priority applications are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was supported, in whole or in part, by Program Project Grant Nos. P01CA76259, P01CA81534 and P30CA56036 from the National Cancer Institute. The Government has certain rights in this invention.

BACKGROUND OF THE INVENTION

Cancer, the uncontrolled growth of malignant cells, is a major health problem of the modern medical era and is one of the leading causes of death in developed countries. In the United States, one in four deaths is caused by cancer (Jemal, A. et al., CA Cancer J. Clin. 52:23-47 (2002)). Among cancers, those that arise from organs and solid tissues, known as solid cancers (e.g., colon cancer, lung cancer, breast cancer, stomach cancer, prostate cancer, pancreatic cancer) are among the most-commonly identified human cancers.

For example, prostate cancer is the most frequently diagnosed noncutaneous malignancy among men in industrialized countries, and, in the United States, 1 in 8 men will develop prostate cancer during his life (Simard, J. et al., Endocrinology 143(6):2029-40 (2002)). The incidence of prostate cancer has dramatically increased over the last decades and prostate cancer is now a leading cause of death in the United States and Western Europe (Peschel, R. E. and J. W. Colberg, Lancet 4:233-41 (2003); Nelson, W. G. et al., N. Engl. J. Med. 349(4):366-81 (2003)). An average 40% reduction in life expectancy affects males with prostate cancer. If detected early, prior to metastasis and local spread beyond the capsule, prostate cancer can often times be cured (e.g., using surgery). However, if diagnosed after spread and metastasis from the prostate, prostate cancer is typically a fatal disease with low cure rates. While prostate-specific antigen (PSA)-based screening has aided early diagnosis of prostate cancer, it is neither highly sensitive nor specific (Punglia et al., N. Engl. J. Med. 349(4):335-42 (2003)). This means that a high percentage of false negative and false positive diagnoses are associated with the test. The consequences are both many instances of missed cancers and unnecessary follow-up biopsies for those without cancer.

Breast cancer remains the second leading cause of cancer-related deaths in women, affecting more than 180,000 women in the United States each year. For women in North America, the life-time odds of getting breast cancer are now one in eight. Although the discovery of BRCA1 and BRCA2 were important steps in identifying key genetic factors involved in breast cancer, it has become clear that mutations in BRCA1 and BRCA2 account for only a fraction of inherited susceptibility to breast cancer (Nathanson, K. L., et al., Human Mol. Gen. 10(7):715-720 (2001); Anglican Breast Cancer Study Group. Br. J. Cancer 83(10):1301-08 (2000); and Syrjakoski, K., et al., J. Natl. Cancer Inst. 92:1529-31 (2000)). Despite considerable research into therapies for breast cancer, breast cancer remains difficult to diagnose and treat effectively, and the high mortality observed in breast cancer patients indicates that improvements are needed in the diagnosis, treatment and prevention of the disease.

Excluding skin cancer, colorectal cancer is the third most frequently diagnosed cancer in the United States and Canada (after lung and breast in women, and lung and prostate in men). The American Cancer Society estimates that there will be approximately 145,000 new cases of colorectal cancer diagnosed in the U.S. in 2005. Colorectal cancer is the second leading cause of cancer death among men and women in the United States and Canada (after lung cancer).

The annual incidence of pancreas cancer is nearly equivalent to the annual mortality, estimated to be 31,860 and 31,270, respectively, in the U.S. in 2004. Patients with locally advanced and metastatic pancreas cancer have poor prognosis, and diagnosis generally occurs too late for surgery or radiotherapy to be curative (Burr, H. A., et al., The Oncologist 10(3): 183-190, (2005)). Chemotherapy can provide relief of symptoms for some patients with advanced pancreas cancer, but its impact on survival has been modest to date.

In the United States, more than 20,000 individuals are diagnosed with stomach (gastric) cancer each year. The American Cancer Society estimates that there will be 22,710 new cases of colorectal cancer diagnosed in the U.S. in 2004. Because stomach cancer may occur without symptoms, it may be in advanced stages by the time the diagnosis is made. Treatment is then directed at making the patient more comfortable and improving the quality of life.

Lung cancer causes more deaths worldwide than any other form of cancer (Goodman, G. E., Thorax 57:994-999 (2002)). In the United States, lung cancer is the primary cause of cancer death among both men and women. In 2002, the death rate from lung cancer was an estimated 134,900 deaths, exceeding the combined total for breast, prostate and colon cancer. Id. Lung cancer is also the leading cause of cancer death in all European countries, and numbers of lung cancer-related deaths are rapidly increasing in developing countries as well.

The five-year survival rate among all lung cancer patients, regardless of the stage of disease at diagnosis, is only about 13%. This contrasts with a five-year survival rate of 46% among cases detected while the disease is still localized. However, only 16% of lung cancers are discovered before the disease has spread. Early detection is difficult as clinical symptoms are often not observed until the disease has reached an advanced stage. Despite research into therapies for this and other cancers, lung cancer remains difficult to diagnose and treat effectively.

Clearly, the identification of markers and genes that are responsible for susceptibility to particular forms of solid cancer (e.g., prostate cancer, breast cancer, lung cancer, stomach cancer, colon cancer, pancreatic cancer) is one of the major challenges facing oncology today. There is a need to identify means for the early detection of individuals that have a genetic susceptibility to cancer so that more aggressive screening and intervention regimens may be instituted for the early detection and treatment of cancer. Cancer genes may also reveal key molecular pathways that may be manipulated (e.g., using small or large molecule weight drugs) and may lead to more effective treatments regardless of the cancer stage when a particular cancer is first diagnosed.

MicroRNAs are a class of small, non-coding RNAs that control gene expression by hybridizing to and triggering either translational repression or, less frequently, degradation of a messenger RNA (mRNA) target. The discovery and study of miRNAs has revealed miRNA-mediated gene regulatory mechanisms that play important roles in organismal development and various cellular processes, such as cell differentiation, cell growth and cell death (Cheng, A. M., et al., Nucleic Acids Res. 33:1290-1297 (2005)). Recent studies suggest that aberrant expression of particular miRNAs may be involved in human diseases, such as neurological disorders (Ishizuka, A., et al., Genes Dev. 16:2497-2508 (2002)) and cancer. In particular, misexpression of miR-16-1 and/or miR-15a has been found in human chronic lymphocytic leukemias (Calin, G. A., et al., Proc. Natl. Acad. Sci. U.S.A. 99:15524-15529 (2002)).

Clearly, there is a great need in the art for improved methods for detecting and treating solid cancers (e.g., prostate cancer, breast cancer, lung cancer, stomach cancer, colon cancer, pancreatic cancer). The present invention provides novel methods and compositions for the diagnosis and treatment of solid cancers.

SUMMARY OF THE INVENTION

The present invention is based, in part, on the identification of specific miRNAs that have altered expression levels in particular solid cancers.

Accordingly, the invention encompasses methods of diagnosing whether a subject has, or is at risk for developing, a solid cancer. According to the methods of the invention, the level of at least one miR gene product in a test sample from the subject is compared to the level of a corresponding miR gene product in a control sample. An alteration (e.g., an increase, a decrease) in the level of the miR gene product in the test sample, relative to the level of a corresponding miR gene product in a control sample, is indicative of the subject either having, or being at risk for developing, a solid cancer. The solid cancer can be any cancer that arises from organs and solid tissues. In certain embodiments, the solid cancer is stomach cancer, breast cancer, pancreatic cancer, colon cancer, lung cancer or prostate cancer. In particular embodiments, the solid cancer is not breast cancer, lung cancer, prostate cancer, pancreatic cancer or gastrointestinal cancer.

In one embodiment, the at least one miR gene product measured in the test sample is selected from the group consisting of miR-21, miR-191, miR-17-5p and combinations thereof. In another embodiment, the at least one miR gene product measured in the test sample is selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

In one embodiment, the solid cancer is breast cancer or lung cancer and the at least one miR gene product measured in the test sample is selected from the group consisting of miR-210, miR-213 and a combination thereof.

In another embodiment, the solid cancer is colon cancer, stomach cancer, prostate cancer or pancreas cancer and the at least one miR gene product measured in the test sample is miR-218-2.

In a certain embodiment, the solid cancer is breast cancer and the at least one miR gene product measured in the test sample is selected from the group consisting of miR-125b-1, miR-125b-2, miR-145, miR-21 and combinations thereof. In a related embodiment, the solid cancer is breast cancer and the at least one miR gene product in the test sample is selected from the group consisting of miR-21, miR-29b-2, miR-146, miR-125b-2, miR-125b-1, miR-10b, miR-145, miR-181a, miR-140, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-130a, miR-155, let-7a-2, miR-205, miR-29c, miR-224, miR-100, miR-31, miR-30c, miR-17-5p, miR-210, miR-122a, miR-16-2 and combinations thereof.

In another embodiment, the solid cancer is colon cancer and the at least one miR gene product in the test sample is selected from the group consisting of miR-24-1, miR-29b-2, miR-20a, miR-10a, miR-32, miR-203, miR-106a, miR-17-5p, miR-30c, miR-223, miR-126*, miR-128b, miR-21, miR-24-2, miR-99b prec, miR-155, miR-213, miR-150, miR-107, miR-191, miR-221, miR-9-3 and combinations thereof.

In yet another embodiment, the solid cancer is lung cancer and the miR gene product in the test sample is selected from the group consisting of miR-21, miR-205, miR-200b, miR-9-1, miR-210, miR-148, miR-141, miR-132, miR-215, miR-128b, let-7g, miR-16-2, miR-129-1/2 prec, miR-126*, miR-142-as, miR-30d, miR-30a-5p, miR-7-2, miR-199a-1, miR-127, miR-34a prec, miR-34a, miR-136, miR-202, miR-196-2, miR-199a-2, let-7a-2, miR-124a-1, miR-149, miR-17-5p, miR-196-1 prec, miR-10a, miR-99b prec, miR-196-1, miR-199b, miR-191, miR-195, miR-155 and combinations thereof.

In an additional embodiment, the solid cancer is pancreatic cancer and the at least one miR gene product measured in the test sample is selected from the group consisting of miR-103-1, miR-103-2, miR-155, miR-204 and combinations thereof. In a related embodiment, the solid cancer is pancreatic cancer and the miR gene product in the test sample is selected from the group consisting of miR-103-2, miR-103-1, miR-24-2, miR-107, miR-100, miR-125b-2, miR-125b-1, miR-24-1, miR-191, miR-23a, miR-26a-1, miR-125a, miR-130a, miR-26b, miR-145, miR-221, miR-126*, miR-16-2, miR-146, miR-214, miR-99b, miR-128b, miR-155, miR-29b-2, miR-29a, miR-25, miR-16-1, miR-99a, miR-224, miR-30d, miR-92-2, miR-199a-1, miR-223, miR-29c, miR-30b, miR-129-1/2, miR-197, miR-17-5p, miR-30c, miR-7-1, miR-93-1, miR-140, miR-30a 5p, miR-132, miR-181b-1, miR-152 prec, miR-23b, miR-20a, miR-222, miR-27a, miR-92-1, miR-21, miR-129-1/2 prec, miR-150, miR-32, miR-106a, miR-29b-1 and combinations thereof.

In another embodiment, the solid cancer is prostate cancer and the miR gene product in the test sample is selected from the group consisting of let-7d, miR-128a prec, miR-195, miR-203, let-7a-2 prec, miR-34a, miR-20a, miR-218-2, miR-29a, miR-25, miR-95, miR-197, miR-135-2, miR-187, miR-196-1, miR-148, miR-191, miR-21, let-71, miR-198, miR-199a-2, miR-30c, miR-17-5p, miR-92-2, miR-146, miR-181b-1 prec, miR-32, miR-206, miR-184 prec, miR-29a prec, miR-29b-2, miR-149, miR-181b-1, miR-196-1 prec, miR-93-1, miR-223, miR-16-1, miR-101-1, miR-124a-1, miR-26a-1, miR-214, miR-27a, miR-24-1, miR-106a, miR-199a-1 and combinations thereof.

In yet another embodiment, the solid cancer is stomach cancer and the miR gene product in the test sample is selected from the group consisting of miR-223, miR-21, miR-218-2, miR-103-2, miR-92-2, miR-25, miR-136, miR-191, miR-221, miR-125b-2, miR-103-1, miR-214, miR-222, miR-212 prec, miR-125b-1, miR-100, miR-107, miR-92-1, miR-96, miR-192, miR-23a, miR-215, miR-7-2, miR-138-2, miR-24-1, miR-99b, miR-33b, miR-24-2 and combinations thereof.

The level of the at least one miR gene product can be measured using a variety of techniques that are well known to those of skill in the art (e.g., quantitative or semi-quantitative RT-PCR, Northern blot analysis, solution hybridization detection). In a particular embodiment, the level of at least one miR gene product is measured by reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides, hybridizing the target oligodeoxynucleotides to one or more miRNA-specific probe oligonucleotides (e.g., hybridizing to a microarray that comprises several miRNA-specific probe oligonucleotides) to provide a hybridization profile for the test sample, and comparing the test sample hybridization profile to a hybridization profile from a control sample. An alteration in the signal of at least one miRNA in the test sample relative to the control sample is indicative of the subject either having, or being at risk for developing, a solid cancer. In a particular embodiment, target oligonucleotides are hybridized to a microarray comprising miRNA-specific probe oligonucleotides for one or more miRNAs selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

The invention also encompasses methods of inhibiting tumorigenesis in a subject who has, or is suspected of having, a solid cancer (e.g., prostate cancer, stomach cancer, pancreatic cancer, lung cancer, breast cancer, colon cancer), wherein at least one miR gene product is deregulated (e.g., down-regulated, up-regulated) in the cancer cells of the subject. When the at least one isolated miR gene product is down-regulated in the cancer cells, the method comprises administering an effective amount of an isolated miR gene product, an isolated variant or a biologically-active fragment of the miR gene product or variant, such that proliferation of cancer cells in the subject is inhibited. In a further embodiment, the at least one isolated miR gene product is selected from the group consisting of miR-145, miR-155, miR-218-2 and combinations thereof. In a particular embodiment, the miR gene product is not miR-15a or miR-16-1. When the at least one isolated miR gene product is up-regulated in the cancer cells, the method comprises administering to the subject an effective amount of at least one compound for inhibiting expression of the at least one miR gene product (referred to herein as a “miR expression-inhibition compound”), such that proliferation of cancer cells in the subject is inhibited. In a particular embodiment, the at least one miR expression-inhibition compound is specific for a miR gene product selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

In a related embodiment, the methods of inhibiting tumorigenesis in a subject additionally comprise the step of determining the amount of at least one miR gene product in cancer cells from the subject, and comparing that level of the miR gene product in the cells to the level of a corresponding miR gene product in control cells. If expression of the miR gene product is deregulated (e.g., down-regulated, up-regulated) in cancer cells, the methods further comprise altering the amount of the at least one miR gene product expressed in the cancer cells. In one embodiment, the amount of the miR gene product expressed in the cancer cells is less than the amount of the miR gene product expressed in a control cell (e.g., control cells), and an effective amount of the down-regulated miR gene product, isolated variant or biologically-active fragment of the miR gene product or variant, is administered to the subject. Suitable miR gene products for this embodiment include miR-145, miR-155, miR-218-2 and combinations thereof, among others. In a particular embodiment, the miR gene product is not miR-15a or miR-16-1. In another embodiment, the amount of the miR gene product expressed in the cancer cells is greater than the amount of the miR gene product expressed in the control cell (e.g., control cells), and an effective amount of at least one compound for inhibiting expression of the at least one up-regulated miR gene product is administered to the subject. Suitable compounds for inhibiting expression of the at least one miR gene product include, but are not limited to, compounds that inhibit the expression of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

The invention further provides pharmaceutical compositions for treating solid cancers (e.g., prostate cancer, stomach cancer, pancreatic cancer, lung cancer, breast cancer, colon cancer). In one embodiment, the pharmaceutical compositions comprise at least one isolated miR gene product and a pharmaceutically-acceptable carrier. In a particular embodiment, the at least one miR gene product corresponds to a miR gene product that has a decreased level of expression in cancer cells relative to control cells. In certain embodiments the isolated miR gene product is selected from the group consisting of miR-145, miR-155, miR-218-2 and combinations thereof.

In another embodiment, the pharmaceutical compositions of the invention comprise at least one miR expression-inhibition compound and a pharmaceutically-acceptable carrier. In a particular embodiment, the at least one miR expression-inhibition compound is specific for a miR gene product whose expression is greater in cancer cells than in control cells. In certain embodiments, the miR expression-inhibition compound is specific for one or more miR gene products selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

The invention also encompasses methods of identifying an inhibitor of tumorigenesis, comprising providing a test agent to a cell and measuring the level of at least one miR gene product in the cell. In one embodiment, the method comprises providing a test agent to a cell and measuring the level of at least one miR gene product associated with decreased expression levels in solid cancers (e.g., prostate cancer, stomach cancer, pancreatic cancer, lung cancer, breast cancer, colon cancer). An increase in the level of the miR gene product in the cell, relative to a suitable control cell, is indicative of the test agent being an inhibitor of tumorigenesis. In a particular embodiment, the at least one miR gene product associated with decreased expression levels in solid cancer cells is selected from the group consisting of miR-145, miR-155, miR-218-2 and combinations thereof.

In other embodiments, the method comprises providing a test agent to a cell and measuring the level of at least one miR gene product associated with increased expression levels in solid cancers. A decrease in the level of the miR gene product in the cell, relative to a suitable control cell, is indicative of the test agent being an inhibitor of tumorigenesis. In a particular embodiment, the at least one miR gene product associated with increased expression levels in solid cancer cells is selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 depicts a clustering analysis of 540 samples, representing 6 solid cancers (top) and the respective normal tissues. miRNAs included in the tree (n=137) represent those whose expression level (background-subtracted intensity) was higher than the threshold value (256) in at least 50% of the samples analyzed. Arrays were median-centered and normalized using Gene Cluster 2.0. Average linkage clustering was performed by using uncentered correlation metric. The colors indicate the difference in expression level from the median for the microRNAs in each sample.

FIG. 2 depicts unsupervised analysis of microRNA expression data. MicroRNA profiling of 540 samples (indicated at top of panel) covering breast, colon, lung, pancreas, prostate and stomach (normal tissues and tumors) were filtered, centered and normalized for each feature. The data were subject to hierarchical clustering on both the samples (horizontally-oriented) and the features (vertically-oriented with average linkage and Pearson correlation as a similarity measure. Sample names are indicated at the top of the figure and miRNA names on the left. The probe ID is indicated in parentheses, as the same microRNA can be measured by different oligonucleotides. The colors indicate the difference in expression level from the median for the microRNAs in each sample.

FIG. 3 depicts the expression of differentially-regulated miRNAs across solid cancers (top). Sixty-one microRNAs, which are present in at least 90% of the tissues solid cancers, are represented (right of panel). The tree displays the average absolute expression values for each of the listed microRNAs after log₂ transformation. The mean was computed over all samples from the same tissue or tumor histotype. Genes were mean-centered and normalized using Gene Cluster 2.0. Average linkage clustering was performed using Euclidean distance.

FIG. 4 depicts fold changes in the expression of miRNAs present in at least 75% of the solid tumors with at least 1 tumor absolute value higher than 2 in different cancer samples (top), relative to normal samples. The tree displays the log₂ transformation of average fold changes (cancer vs. normal). The mean was computed over all samples from the same tissue or tumor histotype. Arrays were mean-centered and normalized using Gene Cluster 2.0. Average linkage clustering was performed using uncentered correlation metric.

FIG. 5 depicts fold changes in the expression of miRNAs present in the signatures of at least 50% of the solid tumors in cancer vs. normal samples. The tree displays the log₂ transformation of the average fold changes (cancer over normal). The mean was computed over all samples from the same tissue or tumor histotype. Arrays were mean centered and normalized using Gene Cluster 2.0. Average linkage clustering was performed using uncentered correlation metric.

FIG. 6A depicts bar graphs indicating that the 3′UTR of different genes encoding cancer protein enables cancer regulation by microRNA. The relative repression of firefly luciferase expression (Fold Change) standardized to a renilla luciferase control. PLAG1, pleiomorphic adenoma gene 1; TGFBR2, transforming growth factor beta receptor II; Rb, retinoblastoma gene. pGL-3 (Promega) was used as the empty vector. miR-20a, miR-26a-1 and miR-106 oligoRNAs (sense and scrambled) were used for transfections. A second experiment using mutated versions of each target mRNA, which lack the 5′ miRNA-end complementarity site (MUT), as controls is shown in the bottom panel. All the experiments were performed twice in triplicate (n=6).

FIG. 6B depicts Western blots indicating that, in certain cancers (e.g., lung, breast, colon, gastric), the levels of RB1 (Rb) protein displays an inverse correlation with the level of miR-106a expression. β-Actin was used as a control for normalization. N1, normal sample; T1 and T2, tumor sample.

FIG. 7 depicts Northern blots showing down-regulation of miR-145 (top) and up-regulation of miR-21 (bottom) expression in breast cancer samples (P series and numbered series) relative to normal samples. Normalization was performed with a U6-specific probe.

FIG. 8 depicts Northern blots showing up-regulation of miR-103 and down-regulation miR-155 (top) expression in different endocrine pancreatic cancer samples (WDET, well differentiated pancreatic endocrine tumors, WDEC, well differentiated pancreatic endocrine carcinomas and ACC, pancreatic acinar cell carcinomas) relative to normal samples (K series), as well as up-regulation of miR-204 (bottom) expression in insulinomas (F series) relative to normal samples (K series) and non secreting/non functioning (NF-series) samples. Normalization was performed with a probe specific to 5S RNA.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based, in part, on the identification of particular microRNAs whose expression is altered in cancer cells associated with different solid cancers, such as colon, stomach, pancreatic, lung, breast and prostate cancer, relative to normal control cells.

As used herein interchangeably, a “miR gene product,” “microRNA,” “miR,” or “miRNA” refers to the unprocessed (e.g., precursor) or processed (e.g., mature) RNA transcript from a miR gene. As the miR gene products are not translated into protein, the term “miR gene products” does not include proteins. The unprocessed miR gene transcript is also called a “miR precursor” or “miR prec” and typically comprises an RNA transcript of about 70-100 nucleotides in length. The miR precursor can be processed by digestion with an RNAse (for example, Dicer, Argonaut, or RNAse III (e.g., E. coli RNAse III)) into an active 19-25 nucleotide RNA molecule. This active 19-25 nucleotide RNA molecule is also called the “processed” miR gene transcript or “mature” miRNA.

The active 19-25 nucleotide RNA molecule can be obtained from the miR precursor through natural processing routes (e.g., using intact cells or cell lysates) or by synthetic processing routes (e.g., using isolated processing enzymes, such as isolated Dicer, Argonaut, or RNAse III). It is understood that the active 19-25 nucleotide RNA molecule can also be produced directly by biological or chemical synthesis, without having been processed from the miR precursor. When a microRNA is referred to herein by name, the name corresponds to both the precursor and mature forms, unless otherwise indicated.

Tables 1a and 1b depict the nucleotide sequences of particular precursor and mature human microRNAs.

TABLE 1a Human microRNA Precursor Sequences SEQ Precursor ID Name Sequence (5′ To 3′)* NO. let-7a-1 CACUGUGGGAUGAGGUAGUAGGUUGUAUAGUUU   1 UAGGGUCACACCCACCACUGGGAGAUAACUAUA CAAUCUACUGUCUUUCCUAACGUG let-7a-2 AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUU   2 ACAUCAAGGGAGAUAACUGUACAGCCUCCUAGC UUUCCU let-7a-3 GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUC   3 UGCCCUGCUAUGGGAUAACUAUACAAUCUACUG UCUUUCCU let-7a-4 GUGACUGCAUGCUCCCAGGUUGAGGUAGUAGGU   4 UGUAUAGUUUAGAAUUACACAAGGGAGAUAACU GUACAGCCUCCUAGCUUUCCUUGGGUCUUGCAC UAAACAAC let-7b GGCGGGGUGAGGUAGUAGGUUGUGUGGUUUCAG   5 GGCAGUGAUGUUGCCCCUCGGAAGAUAACUAUA CAACCUACUGCCUUCCCUG let-7c GCAUCCGGGUUGAGGUAGUAGGUUGUAUGGUUU   6 AGAGUUACACCCUGGGAGUUAACUGUACAACCU UCUAGCUUUCCUUGGAGC let-7d CCUAGGAAGAGGUAGUAGGUUGCAUAGUUUUAG   7 GGCAGGGAUUUUGCCCACAAGGAGGUAACUAUA CGACCUGCUGCCUUUCUUAGG let-7d-v1 CUAGGAAGAGGUAGUAGUUUGCAUAGUUUUAGG   8 GCAAAGAUUUUGCCCACAAGUAGUUAGCUAUAC GACCUGCAGCCUUUUGUAG let-7d-v2 CUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGG   9 GUUGUGACAUUGCCCGCUGUGGAGAUAACUGCG CAAGCUACUGCCUUGCUAG let-7e CCCGGGCUGAGGUAGGAGGUUGUAUAGUUGAGG  10 AGGACACCCAAGGAGAUCACUAUACGGCCUCCU AGCUUUCCCCAGG let-7f-1 UCAGAGUGAGGUAGUAGAUUGUAUAGUUGUGGG  11 GUAGUGAUUUUACCCUGUUCAGGAGAUAACUAU ACAAUCUAUUGCCUUCCCUGA let-7f-2-1 CUGUGGGAUGAGGUAGUAGAUUGUAUAGUUGUG  12 GGGUAGUGAUUUUACCCUGUUCAGGAGAUAACU AUACAAUCUAUUGCCUUCCCUGA let-7f-2-2 CUGUGGGAUGAGGUAGUAGAUUGUAUAGUUUUA  13 GGGUCAUACCCCAUCUUGGAGAUAACUAUACAG UCUACUGUCUUUCCCACGG let-7g UUGCCUGAUUCCAGGCUGAGGUAGUAGUUUGUA  14 CAGUUUGAGGGUCUAUGAUACCACCCGGUACAG GAGAUAACUGUACAGGCCACUGCCUUGCCAGGA ACAGCGCGC let-7i CUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGG  15 GUUGUGACAUUGCCCGCUGUGGAGAUAACUGCG CAAGCUACUGCCUUGCUAG miR-1b-1-1 ACCUACUCAGAGUACAUACUUCUUUAUGUACCC  16 AUAUGAACAUACAAUGCUAUGGAAUGUAAAGAA GUAUGUAUUUUUGGUAGGC miR-1b-1-2 CAGCUAACAACUUAGUAAUACCUACUCAGAGUA  17 CAUACUUCUUUAUGUACCCAUAUGAACAUACAA UGCUAUGGAAUGUAAAGAAGUAUGUAUUUUUGG UAGGCAAUA miR-1b-2 GCCUGCUUGGGAAACAUACUUCUUUAUAUGCCC  18 AUAUGGACCUGCUAAGCUAUGGAAUGUAAAGAA GUAUGUAUCUCAGGCCGGG miR-1b UGGGAAACAUACUUCUUUAUAUGCCCAUAUGGA  19 CCUGCUAAGCUAUGGAAUGUAAAGAAGUAUGUA UCUCA miR-1d ACCUACUCAGAGUACAUACUUCUUUAUGUACCC  20 AUAUGAACAUACAAUGCUAUGGAAUGUAAAGAA GUAUGUAUUUUUGGUAGGC miR-7-1a UGGAUGUUGGCCUAGUUCUGUGUGGAAGACUAG  21 UGAUUUUGUUGUUUUUAGAUAACUAAAUCGACA ACAAAUCACAGUCUGCCAUAUGGCACAGGCCAU GCCUCUACA miR-7-1b UUGGAUGUUGGCCUAGUUCUGUGUGGAAGACUA  22 GUGAUUUUGUUGUUUUUAGAUAACUAAAUCGAC AACAAAUCACAGUCUGCCAUAUGGCACAGGCCA UGCCUCUACAG miR-7-2 CUGGAUACAGAGUGGACCGGCUGGCCCCAUCUG  23 GAAGACUAGUGAUUUUGUUGUUGUCUUACUGCG CUCAACAACAAAUCCCAGUCUACCUAAUGGUGC CAGCCAUCGCA miR-7-3 AGAUUAGAGUGGCUGUGGUCUAGUGCUGUGUGG  24 AAGACUAGUGAUUUUGUUGUUCUGAUGUACUAC GACAACAAGUCACAGCCGGCCUCAUAGCGCAGA CUCCCUUCGAC miR-9-1 CGGGGUUGGUUGUUAUCUUUGGUUAUCUAGCUG  25 UAUGAGUGGUGUGGAGUCUUCAUAAAGCUAGAU AACCGAAAGUAAAAAUAACCCCA miR-9-2 GGAAGCGAGUUGUUAUCUUUGGUUAUCUAGCUG  26 UAUGAGUGUAUUGGUCUUCAUAAAGCUAGAUAA CCGAAAGUAAAAACUCCUUCA miR-9-3 GGAGGCCCGUUUCUCUCUUUGGUUAUCUAGCUG  27 UAUGAGUGCCACAGAGCCGUCAUAAAGCUAGAU AACCGAAAGUAGAAAUGAUUCUCA miR-10a GAUCUGUCUGUCUUCUGUAUAUACCCUGUAGAU  28 CCGAAUUUGUGUAAGGAAUUUUGUGGUCACAAA UUCGUAUCUAGGGGAAUAUGUAGUUGACAUAAA CACUCCGCUCU miR-10b CCAGAGGUUGUAACGUUGUCUAUAUAUACCCUG  29 UAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCA CAGAUUCGAUUCUAGGGGAAUAUAUGGUCGAUG CAAAAACUUCA miR-15a-2 GCGCGAAUGUGUGUUUAAAAAAAAUAAAACCUU  30 GGAGUAAAGUAGCAGCACAUAAUGGUUUGUGGA UUUUGAAAAGGUGCAGGCCAUAUUGUGCUGCCU CAAAAAUAC miR-15a CCUUGGAGUAAAGUAGCAGCACAUAAUGGUUUG  31 UGGAUUUUGAAAAGGUGCAGGCCAUAUUGUGCU GCCUCAAAAAUACAAGG miR-15b-1 CUGUAGCAGCACAUCAUGGUUUACAUGCUACAG  32 UCAAGAUGCGAAUCAUUAUUUGCUGCUCUAG miR-15b-2 UUGAGGCCUUAAAGUACUGUAGCAGCACAUCAU  33 GGUUUACAUGCUACAGUCAAGAUGCGAAUCAUU AUUUGCUGCUCUAGAAAUUUAAGGAAAUUCAU miR-16-1 GUCAGCAGUGCCUUAGCAGCACGUAAAUAUUGG  34 CGUUAAGAUUCUAAAAUUAUCUCCAGUAUUAAC UGUGCUGCUGAAGUAAGGUUGAC miR-16-2 GUUCCACUCUAGCAGCACGUAAAUAUUGGCGUA  35 GUGAAAUAUAUAUUAAACACCAAUAUUACUGUG CUGCUUUAGUGUGAC miR-16-13 GCAGUGCCUUAGCAGCACGUAAAUAUUGGCGUU  36 AAGAUUCUAAAAUUAUCUCCAGUAUUAACUGUG CUGCUGAAGUAAGGU miR-17 GUCAGAAUAAUGUCAAAGUGCUUACAGUGCAGG  37 UAGUGAUAUGUGCAUCUACUGCAGUGAAGGCAC UUGUAGCAUUAUGGUGAC miR-18 UGUUCUAAGGUGCAUCUAGUGCAGAUAGUGAAG  38 UAGAUUAGCAUCUACUGCCCUAAGUGCUCCUUC UGGCA miR-18-13 UUUUUGUUCUAAGGUGCAUCUAGUGCAGAUAGU  39 GAAGUAGAUUAGCAUCUACUGCCCUAAGUGCUC CUUCUGGCAUAAGAA miR-19a GCAGUCCUCUGUUAGUUUUGCAUAGUUGCACUA  40 CAAGAAGAAUGUAGUUGUGCAAAUCUAUGCAAA ACUGAUGGUGGCCUGC miR-19a-13 CAGUCCUCUGUUAGUUUUGCAUAGUUGCACUAC  41 AAGAAGAAUGUAGUUGUGCAAAUCUAUGCAAAA CUGAUGGUGGCCUG miR-19b-1 CACUGUUCUAUGGUUAGUUUUGCAGGUUUGCAU  42 CCAGCUGUGUGAUAUUCUGCUGUGCAAAUCCAU GCAAAACUGACUGUGGUAGUG miR-19b-2 ACAUUGCUACUUACAAUUAGUUUUGCAGGUUUG  43 CAUUUCAGCGUAUAUAUGUAUAUGUGGCUGUGC AAAUCCAUGCAAAACUGAUUGUGAUAAUGU miR-19b-13 UUCUAUGGUUAGUUUUGCAGGUUUGCAUCCAGC  44 UGUGUGAUAUUCUGCUGUGCAAAUCCAUGCAAA ACUGACUGUGGUAG miR-19b-X UUACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG  45 UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGC AAAACUGAUUGUGAU miR-20 GUAGCACUAAAGUGCUUAUAGUGCAGGUAGUGU  46 (miR-20a) UUAGUUAUCUACUGCAUUAUGAGCACUUAAAGU ACUGC miR-21 UGUCGGGUAGCUUAUCAGACUGAUGUUGACUGU  47 UGAAUCUCAUGGCAACACCAGUCGAUGGGCUGU CUGACA miR-21-17 ACCUUGUCGGGUAGCUUAUCAGACUGAUGUUGA  48 CUGUUGAAUCUCAUGGCAACACCAGUCGAUGGG CUGUCUGACAUUUUG miR-22 GGCUGAGCCGCAGUAGUUCUUCAGUGGCAAGCU  49 UUAUGUCCUGACCCAGCUAAAGCUGCCAGUUGA AGAACUGUUGCCCUCUGCC miR-23a GGCCGGCUGGGGUUCCUGGGGAUGGGAUUUGCU  50 UCCUGUCACAAAUCACAUUGCCAGGGAUUUCCA ACCGACC miR-23b CUCAGGUGCUCUGGCUGCUUGGGUUCCUGGCAU  51 GCUGAUUUGUGACUUAAGAUUAAAAUCACAUUG CCAGGGAUUACCACGCAACCACGACCUUGGC miR-23-19 CCACGGCCGGCUGGGGUUCCUGGGGAUGGGAUU  52 UGCUUCCUGUCACAAAUCACAUUGCCAGGGAUU UCCAACCGACCCUGA miR-24-1 CUCCGGUGCCUACUGAGCUGAUAUCAGUUCUCA  53 UUUUACACACUGGCUCAGUUCAGCAGGAACAGG AG miR-24-2 CUCUGCCUCCCGUGCCUACUGAGCUGAAACACAG  54 UUGGUUUGUGUACACUGGCUCAGUUCAGCAGGA ACAGGG miR-24-19 CCCUGGGCUCUGCCUCCCGUGCCUACUGAGCUGA  55 AACACAGUUGGUUUGUGUACACUGGCUCAGUUC AGCAGGAACAGGGG miR-24-9 CCCUCCGGUGCCUACUGAGCUGAUAUCAGUUCU  56 CAUUUUACACACUGGCUCAGUUCAGCAGGAACA GCAUC miR-25 GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUU  57 GCUGGACGCUGCCCUGGGCAUUGCACUUGUCUC GGUCUGACAGUGCCGGCC miR-26a AGGCCGUGGCCUCGUUCAAGUAAUCCAGGAUAG  58 GCUGUGCAGGUCCCAAUGGCCUAUCUUGGUUAC UUGCACGGGGACGCGGGCCU miR-26a-1 GUGGCCUCGUUCAAGUAAUCCAGGAUAGGCUGU  59 GCAGGUCCCAAUGGGCCUAUUCUUGGUUACUUG CACGGGGACGC miR-26a-2 GGCUGUGGCUGGAUUCAAGUAAUCCAGGAUAGG  60 CUGUUUCCAUCUGUGAGGCCUAUUCUUGAUUAC UUGUUUCUGGAGGCAGCU miR-26b CCGGGACCCAGUUCAAGUAAUUCAGGAUAGGUU  61 GUGUGCUGUCCAGCCUGUUCUCCAUUACUUGGC UCGGGGACCGG miR-27a CUGAGGAGCAGGGCUUAGCUGCUUGUGAGCAGG  62 GUCCACACCAAGUCGUGUUCACAGUGGCUAAGU UCCGCCCCCCAG miR-27b-1 AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGA  63 UUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUC UGCACCU miR-27b-2 ACCUCUCUAACAAGGUGCAGAGCUUAGCUGAUU  64 GGUGAACAGUGAUUGGUUUCCGCUUUGUUCACA GUGGCUAAGUUCUGCACCUGAAGAGAAGGUG miR-27-19 CCUGAGGAGCAGGGCUUAGCUGCUUGUGAGCAG  65 GGUCCACACCAAGUCGUGUUCACAGUGGCUAAG UUCCGCCCCCCAGG miR-28 GGUCCUUGCCCUCAAGGAGCUCACAGUCUAUUG  66 AGUUACCUUUCUGACUUUCCCACUAGAUUGUGA GCUCCUGGAGGGCAGGCACU miR-29a-2 CCUUCUGUGACCCCUUAGAGGAUGACUGAUUUC  67 UUUUGGUGUUCAGAGUCAAUAUAAUUUUCUAGC ACCAUCUGAAAUCGGUUAUAAUGAUUGGGGAAG AGCACCAUG miR-29a AUGACUGAUUUCUUUUGGUGUUCAGAGUCAAUA  68 UAAUUUUCUAGCACCAUCUGAAAUCGGUUAU miR-29b-1 CUUCAGGAAGCUGGUUUCAUAUGGUGGUUUAGA  69 UUUAAAUAGUGAUUGUCUAGCACCAUUUGAAAU CAGUGUUCUUGGGGG miR-29b-2 CUUCUGGAAGCUGGUUUCACAUGGUGGCUUAGA  70 UUUUUCCAUCUUUGUAUCUAGCACCAUUUGAAA UCAGUGUUUUAGGAG miR-29c ACCACUGGCCCAUCUCUUACACAGGCUGACCGAU  71 UUCUCCUGGUGUUCAGAGUCUGUUUUUGUCUAG CACCAUUUGAAAUCGGUUAUGAUGUAGGGGGAA AAGCAGCAGC miR-30a GCGACUGUAAACAUCCUCGACUGGAAGCUGUGA  72 AGCCACAGAUGGGCUUUCAGUCGGAUGUUUGCA GCUGC miR-30b-1 AUGUAAACAUCCUACACUCAGCUGUAAUACAUG  73 GAUUGGCUGGGAGGUGGAUGUUUACGU miR-30b-2 ACCAAGUUUCAGUUCAUGUAAACAUCCUACACU  74 CAGCUGUAAUACAUGGAUUGGCUGGGAGGUGGA UGUUUACUUCAGCUGACUUGGA miR-30c AGAUACUGUAAACAUCCUACACUCUCAGCUGUG  75 GAAAGUAAGAAAGCUGGGAGAAGGCUGUUUACU CUUUCU miR-30d GUUGUUGUAAACAUCCCCGACUGGAAGCUGUAA  76 GACACAGCUAAGCUUUCAGUCAGAUGUUUGCUG CUAC miR-30e CUGUAAACAUCCUUGACUGGAAGCUGUAAGGUG  77 UUCAGAGGAGCUUUCAGUCGGAUGUUUACAG miR-31 GGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGA  78 ACUGGGAACCUGCUAUGCCAACAUAUUGCCAUC UUUCC miR-32 GGAGAUAUUGCACAUUACUAAGUUGCAUGUUGU  79 CACGGCCUCAAUGCAAUUUAGUGUGUGUGAUAU UUUC miR-33b GGGGGCCGAGAGAGGCGGGCGGCCCCGCGGUGC  80 AUUGCUGUUGCAUUGCACGUGUGUGAGGCGGGU GCAGUGCCUCGGCAGUGCAGCCCGGAGCCGGCCC CUGGCACCAC miR-33b-2 ACCAAGUUUCAGUUCAUGUAAACAUCCUACACU  81 CAGCUGUAAUACAUGGAUUGGCUGGGAGGUGGA UGUUUACUUCAGCUGACUUGGA miR-33 CUGUGGUGCAUUGUAGUUGCAUUGCAUGUUCUG  82 GUGGUACCCAUGCAAUGUUUCCACAGUGCAUCA CAG miR-34-a GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUU  83 AGCUGGUUGUUGUGAGCAAUAGUAAGGAAGCAA UCAGCAAGUAUACUGCCCUAGAAGUGCUGCACG UUGUGGGGCCC miR-34-b GUGCUCGGUUUGUAGGCAGUGUCAUUAGCUGAU  84 UGUACUGUGGUGGUUACAAUCACUAACUCCACU GCCAUCAAAACAAGGCAC miR-34-c AGUCUAGUUACUAGGCAGUGUAGUUAGCUGAUU  85 GCUAAUAGUACCAAUCACUAACCACACGGCCAG GUAAAAAGAUU miR-91-13 UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGU  86 AGUGAUAUGUGCAUCUACUGCAGUGAAGGCACU UGUAGCAUUAUGGUGA miR-92-1 CUUUCUACACAGGUUGGGAUCGGUUGCAAUGCU  87 GUGUUUCUGUAUGGUAUUGCACUUGUCCCGGCC UGUUGAGUUUGG miR-92-2 UCAUCCCUGGGUGGGGAUUUGUUGCAUUACUUG  88 UGUUCUAUAUAAAGUAUUGCACUUGUCCCGGCC UGUGGAAGA miR-93-1 CUGGGGGCUCCAAAGUGCUGUUCGUGCAGGUAG  89 (miR-93-2) UGUGAUUACCCAACCUACUGCUGAGCUAGCACU UCCCGAGCCCCCGG miR-95-4 AACACAGUGGGCACUCAAUAAAUGUCUGUUGAA  90 UUGAAAUGCGUUACAUUCAACGGGUAUUUAUUG AGCACCCACUCUGUG miR-96-7 UGGCCGAUUUUGGCACUAGCACAUUUUUGCUUG  91 UGUCUCUCCGCUCUGAGCAAUCAUGUGCAGUGC CAAUAUGGGAAA miR-97-6 GUGAGCGACUGUAAACAUCCUCGACUGGAAGCU  92 (miR-30*) GUGAAGCCACAGAUGGGCUUUCAGUCGGAUGUU UGCAGCUGCCUACU miR-98 GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGG  93 GAUAUUAGGCCCCAAUUAGAAGAUAACUAUACA ACUUACUACUUUCC miR-99b GGCACCCACCCGUAGAACCGACCUUGCGGGGCCU  94 UCGCCGCACACAAGCUCGUGUCUGUGGGUCCGU GUC miR-99a CCCAUUGGCAUAAACCCGUAGAUCCGAUCUUGU  95 GGUGAAGUGGACCGCACAAGCUCGCUUCUAUGG GUCUGUGUCAGUGUG miR-100- AAGAGAGAAGAUAUUGAGGCCUGUUGCCACAAA  96 1/2 CCCGUAGAUCCGAACUUGUGGUAUUAGUCCGCA CAAGCUUGUAUCUAUAGGUAUGUGUCUGUUAGG CAAUCUCAC miR-100- CCUGUUGCCACAAACCCGUAGAUCCGAACUUGU  97 11 GGUAUUAGUCCGCACAAGCUUGUAUCUAUAGGU AUGUGUCUGUUAGG miR-101- AGGCUGCCCUGGCUCAGUUAUCACAGUGCUGAU  98 1/2 GCUGUCUAUUCUAAAGGUACAGUACUGUGAUAA CUGAAGGAUGGCAGCCAUCUUACCUUCCAUCAG AGGAGCCUCAC miR-101 UCAGUUAUCACAGUGCUGAUGCUGUCCAUUCUA  99 AAGGUACAGUACUGUGAUAACUGA miR-101-1 UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUG 100 UCUAUUCUAAAGGUACAGUACUGUGAUAACUGA AGGAUGGCA miR-101-2 ACUGUCCUUUUUCGGUUAUCAUGGUACCGAUGC 101 UGUAUAUCUGAAAGGUACAGUACUGUGAUAACU GAAGAAUGGUGGU miR-101-9 UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUG 102 UAUAUCUGAAAGGUACAGUACUGUGAUAACUGA AGAAUGGUG miR-102-1 CUUCUGGAAGCUGGUUUCACAUGGUGGCUUAGA 103 UUUUUCCAUCUUUGUAUCUAGCACCAUUUGAAA UCAGUGUUUUAGGAG miR-102- CUUCAGGAAGCUGGUUUCAUAUGGUGGUUUAGA 104 7.1 UUUAAAUAGUGAUUGUCUAGCACCAUUUGAAAU (miR-102- CAGUGUUCUUGGGGG 7.2) miR-103-2 UUGUGCUUUCAGCUUCUUUACAGUGCUGCCUUG 105 UAGCAUUCAGGUCAAGCAACAUUGUACAGGGCU AUGAAAGAACCA miR-103-1 UACUGCCCUCGGCUUCUUUACAGUGCUGCCUUG 106 UUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCU AUGAAGGCAUUG miR-104-17 AAAUGUCAGACAGCCCAUCGACUGGUGUUGCCA 107 UGAGAUUCAACAGUCAACAUCAGUCUGAUAAGC UACCCGACAAGG miR-105-1 UGUGCAUCGUGGUCAAAUGCUCAGACUCCUGUG 108 GUGGCUGCUCAUGCACCACGGAUGUUUGAGCAU GUGCUACGGUGUCUA miR-105-2 UGUGCAUCGUGGUCAAAUGCUCAGACUCCUGUG 109 GUGGCUGCUUAUGCACCACGGAUGUUUGAGCAU GUGCUAUGGUGUCUA miR-106-a CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGU 110 AGCUUUUUGAGAUCUACUGCAAUGUAAGCACUU CUUACAUUACCAUGG miR-106-b CCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUA 111 GUGGUCCUCUCCGUGCUACCGCACUGUGGGUAC UUGCUGCUCCAGCAGG miR-107 CUCUCUGCUUUCAGCUUCUUUACAGUGUUGCCU 112 UGUGGCAUGGAGUUCAAGCAGCAUUGUACAGGG CUAUCAAAGCACAGA miR-108-1- ACACUGCAAGAACAAUAAGGAUUUUUAGGGGCA 113 small UUAUGACUGAGUCAGAAAACACAGCUGCCCCUG AAAGUCCCUCAUUUUUCUUGCUGU miR-108-2- ACUGCAAGAGCAAUAAGGAUUUUUAGGGGCAUU 114 small AUGAUAGUGGAAUGGAAACACAUCUGCCCCCAA AAGUCCCUCAUUUU miR-122a-1 CCUUAGCAGAGCUGUGGAGUGUGACAAUGGUGU 115 UUGUGUCUAAACUAUCAAACGCCAUUAUCACAC UAAAUAGCUACUGCUAGGC miR-122a-2 AGCUGUGGAGUGUGACAAUGGUGUUUGUGUCCA 116 AACUAUCAAACGCCAUUAUCACACUAAAUAGCU miR-123 ACAUUAUUACUUUUGGUACGCGCUGUGACACUU 117 CAAACUCGUACCGUGAGUAAUAAUGCGC miR-124a-1 AGGCCUCUCUCUCCGUGUUCACAGCGGACCUUG 118 AUUUAAAUGUCCAUACAAUUAAGGCACGCGGUG AAUGCCAAGAAUGGGGCUG miR-124a-2 AUCAAGAUUAGAGGCUCUGCUCUCCGUGUUCAC 119 AGCGGACCUUGAUUUAAUGUCAUACAAUUAAGG CACGCGGUGAAUGCCAAGAGCGGAGCCUACGGC UGCACUUGAAG miR-124a-3 UGAGGGCCCCUCUGCGUGUUCACAGCGGACCUU 120 GAUUUAAUGUCUAUACAAUUAAGGCACGCGGUG AAUGCCAAGAGAGGCGCCUCC miR-124a CUCUGCGUGUUCACAGCGGACCUUGAUUUAAUG 121 UCUAUACAAUUAAGGCACGCGGUGAAUGCCAAG AG miR-124b CUCUCCGUGUUCACAGCGGACCUUGAUUUAAUG 122 UCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA G miR-125a-1 UGCCAGUCUCUAGGUCCCUGAGACCCUUUAACC 123 UGUGAGGACAUCCAGGGUCACAGGUGAGGUUCU UGGGAGCCUGGCGUCUGGCC miR-125a-2 GGUCCCUGAGACCCUUUAACCUGUGAGGACAUC 124 CAGGGUCACAGGUGAGGUUCUUGGGAGCCUGG miR-125b-1 UGCGCUCCUCUCAGUCCCUGAGACCCUAACUUGU 125 GAUGUUUACCGUUUAAAUCCACGGGUUAGGCUC UUGGGAGCUGCGAGUCGUGCU miR-125b-2 ACCAGACUUUUCCUAGUCCCUGAGACCCUAACU 126 UGUGAGGUAUUUUAGUAACAUCACAAGUCAGGC UCUUGGGACCUAGGCGGAGGGGA miR-126-1 CGCUGGCGACGGGACAUUAUUACUUUUGGUACG 127 CGCUGUGACACUUCAAACUCGUACCGUGAGUAA UAAUGCGCCGUCCACGGCA miR-126-2 ACAUUAUUACUUUUGGUACGCGCUGUGACACUU 128 CAAACUCGUACCGUGAGUAAUAAUGCGC miR-127-1 UGUGAUCACUGUCUCCAGCCUGCUGAAGCUCAG 129 AGGGCUCUGAUUCAGAAAGAUCAUCGGAUCCGU CUGAGCUUGGCUGGUCGGAAGUCUCAUCAUC miR-127-2 CCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCA 130 GAAAGAUCAUCGGAUCCGUCUGAGCUUGGCUGG UCGG miR-128a UGAGCUGUUGGAUUCGGGGCCGUAGCACUGUCU 131 GAGAGGUUUACAUUUCUCACAGUGAACCGGUCU CUUUUUCAGCUGCUUC miR-128b GCCCGGCAGCCACUGUGCAGUGGGAAGGGGGGC 132 CGAUACACUGUACGAGAGUGAGUAGCAGGUCUC ACAGUGAACCGGUCUCUUUCCCUACUGUGUCAC ACUCCUAAUGG miR-128 GUUGGAUUCGGGGCCGUAGCACUGUCUGAGAGG 133 UUUACAUUUCUCACAGUGAACCGGUCUCUUUUU CAGC miR-129-1 UGGAUCUUUUUGCGGUCUGGGCUUGCUGUUCCU 134 CUCAACAGUAGUCAGGAAGCCCUUACCCCAAAA AGUAUCUA miR-129-2 UGCCCUUCGCGAAUCUUUUUGCGGUCUGGGCUU 135 GCUGUACAUAACUCAAUAGCCGGAAGCCCUUAC CCCAAAAAGCAUUUGCGGAGGGCG miR-130a UGCUGCUGGCCAGAGCUCUUUUCACAUUGUGCU 136 ACUGUCUGCACCUGUCACUAGCAGUGCAAUGUU AAAAGGGCAUUGGCCGUGUAGUG miR-131-1 GCCAGGAGGCGGGGUUGGUUGUUAUCUUUGGUU 137 AUCUAGCUGUAUGAGUGGUGUGGAGUCUUCAUA AAGCUAGAUAACCGAAAGUAAAAAUAACCCCAU ACACUGCGCAG miR-131-3 CACGGCGCGGCAGCGGCACUGGCUAAGGGAGGC 138 CCGUUUCUCUCUUUGGUUAUCUAGCUGUAUGAG UGCCACAGAGCCGUCAUAAAGCUAGAUAACCGA AAGUAGAAAUG miR-131 GUUGUUAUCUUUGGUUAUCUAGCUGUAUGAGUG 139 UAUUGGUCUUCAUAAAGCUAGAUAACCGAAAGU AAAAAC miR-132-1 CCGCCCCCGCGUCUCCAGGGCAACCGUGGCUUUC 140 GAUUGUUACUGUGGGAACUGGAGGUAACAGUCU ACAGCCAUGGUCGCCCCGCAGCACGCCCACGCGC miR-132-2 GGGCAACCGUGGCUUUCGAUUGUUACUGUGGGA 141 ACUGGAGGUAACAGUCUACAGCCAUGGUCGCCC miR-133a-1 ACAAUGCUUUGCUAGAGCUGGUAAAAUGGAACC 142 AAAUCGCCUCUUCAAUGGAUUUGGUCCCCUUCA ACCAGCUGUAGCUAUGCAUUGA miR-133a-2 GGGAGCCAAAUGCUUUGCUAGAGCUGGUAAAAU 143 GGAACCAAAUCGACUGUCCAAUGGAUUUGGUCC CCUUCAACCAGCUGUAGCUGUGCAUUGAUGGCG CCG miR-133 GCUAGAGCUGGUAAAAUGGAACCAAAUCGCCUC 144 UUCAAUGGAUUUGGUCCCCUUCAACCAGCUGUA GC miR-133b CCUCAGAAGAAAGAUGCCCCCUGCUCUGGCUGG 145 UCAAACGGAACCAAGUCCGUCUUCCUGAGAGGU UUGGUCCCCUUCAACCAGCUACAGCAGGGCUGG CAAUGCCCAGUCCUUGGAGA miR-133b- GCCCCCUGCUCUGGCUGGUCAAACGGAACCAAG 146 small UCCGUCUUCCUGAGAGGUUUGGUCCCCUUCAAC CAGCUACAGCAGGG miR-134-1 CAGGGUGUGUGACUGGUUGACCAGAGGGGCAUG 147 CACUGUGUUCACCCUGUGGGCCACCUAGUCACCA ACCCUC miR-134-2 AGGGUGUGUGACUGGUUGACCAGAGGGGCAUGC 148 ACUGUGUUCACCCUGUGGGCCACCUAGUCACCA ACCCU miR-135a-1 AGGCCUCGCUGUUCUCUAUGGCUUUUUAUUCCU 149 AUGUGAUUCUACUGCUCACUCAUAUAGGGAUUG GAGCCGUGGCGCACGGCGGGGACA miR-135a-2 AGAUAAAUUCACUCUAGUGCUUUAUGGCUUUUU 150 (miR-135-2) AUUCCUAUGUGAUAGUAAUAAAGUCUCAUGUAG GGAUGGAAGCCAUGAAAUACAUUGUGAAAAAUC A miR-135 CUAUGGCUUUUUAUUCCUAUGUGAUUCUACUGC 151 UCACUCAUAUAGGGAUUGGAGCCGUGG miR-135b CACUCUGCUGUGGCCUAUGGCUUUUCAUUCCUA 152 UGUGAUUGCUGUCCCAAACUCAUGUAGGGCUAA AAGCCAUGGGCUACAGUGAGGGGCGAGCUCC miR-136-1 UGAGCCCUCGGAGGACUCCAUUUGUUUUGAUGA 153 UGGAUUCUUAUGCUCCAUCAUCGUCUCAAAUGA GUCUUCAGAGGGUUCU miR-136-2 GAGGACUCCAUUUGUUUUGAUGAUGGAUUCUUA 154 UGCUCCAUCAUCGUCUCAAAUGAGUCUUC miR-137 CUUCGGUGACGGGUAUUCUUGGGUGGAUAAUAC 155 GGAUUACGUUGUUAUUGCUUAAGAAUACGCGUA GUCGAGG miR-138-1 CCCUGGCAUGGUGUGGUGGGGCAGCUGGUGUUG 156 UGAAUCAGGCCGUUGCCAAUCAGAGAACGGCUA CUUCACAACACCAGGGCCACACCACACUACAGG miR-138-2 CGUUGCUGCAGCUGGUGUUGUGAAUCAGGCCGA 157 CGAGCAGCGCAUCCUCUUACCCGGCUAUUUCACG ACACCAGGGUUGCAUCA miR-138 CAGCUGGUGUUGUGAAUCAGGCCGACGAGCAGC 158 GCAUCCUCUUACCCGGCUAUUUCACGACACCAGG GUUG miR-139 GUGUAUUCUACAGUGCACGUGUCUCCAGUGUGG 159 CUCGGAGGCUGGAGACGCGGCCCUGUUGGAGUA AC miR-140 UGUGUCUCUCUCUGUGUCCUGCCAGUGGUUUUA 160 CCCUAUGGUAGGUUACGUCAUGCUGUUCUACCA CAGGGUAGAACCACGGACAGGAUACCGGGGCAC C miR-140as UCCUGCCAGUGGUUUUACCCUAUGGUAGGUUAC 161 GUCAUGCUGUUCUACCACAGGGUAGAACCACGG ACAGGA miR-140s CCUGCCAGUGGUUUUACCCUAUGGUAGGUUACG 162 UCAUGCUGUUCUACCACAGGGUAGAACCACGGA CAGG miR-141-1 CGGCCGGCCCUGGGUCCAUCUUCCAGUACAGUG 163 UUGGAUGGUCUAAUUGUGAAGCUCCUAACACUG UCUGGUAAAGAUGGCUCCCGGGUGGGUUC miR-141-2 GGGUCCAUCUUCCAGUACAGUGUUGGAUGGUCU 164 AAUUGUGAAGCUCCUAACACUGUCUGGUAAAGA UGGCCC miR-142 ACCCAUAAAGUAGAAAGCACUACUAACAGCACU 165 GGAGGGUGUAGUGUUUCCUACUUUAUGGAUG miR-143-1 GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGU 166 GCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUG AAGCACUGUAGCUCAGGAAGAGAGAAGUUGUUC UGCAGC miR-143-2 CCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUG 167 GGAGUCUGAGAUGAAGCACUGUAGCUCAGG miR-144-1 UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGU 168 AAGUUUGCGAUGAGACACUACAGUAUAGAUGAU GUACUAGUCCGGGCACCCCC miR-144-2 GGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCG 169 AUGAGACACUACAGUAUAGAUGAUGUACUAGUC miR-145-1 CACCUUGUCCUCACGGUCCAGUUUUCCCAGGAA 170 UCCCUUAGAUGCUAAGAUGGGGAUUCCUGGAAA UACUGUUCUUGAGGUCAUGGUU miR-145-2 CUCACGGUCCAGUUUUCCCAGGAAUCCCUUAGA 171 UGCUAAGAUGGGGAUUCCUGGAAAUACUGUUCU UGAG miR-146-1 CCGAUGUGUAUCCUCAGCUUUGAGAACUGAAUU 172 CCAUGGGUUGUGUCAGUGUCAGACCUCUGAAAU UCAGUUCUUCAGCUGGGAUAUCUCUGUCAUCGU miR-146-2 AGCUUUGAGAACUGAAUUCCAUGGGUUGUGUCA 173 GUGUCAGACCUGUGAAAUUCAGUUCUUCAGCU miR-147 AAUCUAAAGACAACAUUUCUGCACACACACCAG 174 ACUAUGGAAGCCAGUGUGUGGAAAUGCUUCUGC UAGAUU miR-148a GAGGCAAAGUUCUGAGACACUCCGACUCUGAGU 175 (miR-148) AUGAUAGAAGUCAGUGCACUACAGAACUUUGUC UC miR-148b CAAGCACGAUUAGCAUUUGAGGUGAAGUUCUGU 176 UAUACACUCAGGCUGUGGCUCUCUGAAAGUCAG UGCAUCACAGAACUUUGUCUCGAAAGCUUUCUA miR-148b- AAGCACGAUUAGCAUUUGAGGUGAAGUUCUGUU 177 small AUACACUCAGGCUGUGGCUCUCUGAAAGUCAGU GCAU miR-149-1 GCCGGCGCCCGAGCUCUGGCUCCGUGUCUUCACU 178 CCCGUGCUUGUCCGAGGAGGGAGGGAGGGACGG GGGCUGUGCUGGGGCAGCUGGA miR-149-2 GCUCUGGCUCCGUGUCUUCACUCCCGUGCUUGUC 179 CGAGGAGGGAGGGAGGGAC miR-150-1 CUCCCCAUGGCCCUGUCUCCCAACCCUUGUACCA 180 GUGCUGGGCUCAGACCCUGGUACAGGCCUGGGG GACAGGGACCUGGGGAC miR-150-2 CCCUGUCUCCCAACCCUUGUACCAGUGCUGGGCU 181 CAGACCCUGGUACAGGCCUGGGGGACAGGG miR-151 UUUCCUGCCCUCGAGGAGCUCACAGUCUAGUAU 182 GUCUCAUCCCCUACUAGACUGAAGCUCCUUGAG GACAGG miR-151-2 CCUGUCCUCAAGGAGCUUCAGUCUAGUAGGGGA 183 UGAGACAUACUAGACUGUGAGCUCCUCGAGGGC AGG miR-152-1 UGUCCCCCCCGGCCCAGGUUCUGUGAUACACUCC 184 GACUCGGGCUCUGGAGCAGUCAGUGCAUGACAG AACUUGGGCCCGGAAGGACC miR-152-2 GGCCCAGGUUCUGUGAUACACUCCGACUCGGGC 185 UCUGGAGCAGUCAGUGCAUGACAGAACUUGGGC CCCGG miR-153- CUCACAGCUGCCAGUGUCAUUUUUGUGAUCUGC 186 1-1 AGCUAGUAUUCUCACUCCAGUUGCAUAGUCACA AAAGUGAUCAUUGGCAGGUGUGGC miR-153- UCUCUCUCUCCCUCACAGCUGCCAGUGUCAUUGU 187 1-2 CACAAAAGUGAUCAUUGGCAGGUGUGGCUGCUG CAUG miR-153- AGCGGUGGCCAGUGUCAUUUUUGUGAUGUUGCA 188 2-1 GCUAGUAAUAUGAGCCCAGUUGCAUAGUCACAA AAGUGAUCAUUGGAAACUGUG miR-153- CAGUGUCAUUUUUGUGAUGUUGCAGCUAGUAAU 189 2-2 AUGAGCCCAGUUGCAUAGUCACAAAAGUGAUCA UUG miR-154-1 GUGGUACUUGAAGAUAGGUUAUCCGUGUUGCCU 190 UCGCUUUAUUUGUGACGAAUCAUACACGGUUGA CCUAUUUUUCAGUACCAA miR-154-2 GAAGAUAGGUUAUCCGUGUUGCCUUCGCUUUAU 191 UUGUGACGAAUCAUACACGGUUGACCUAUUUUU miR-155 CUGUUAAUGCUAAUCGUGAUAGGGGUUUUUGCC 192 UCCAACUGACUCCUACAUAUUAGCAUUAACAG miR-156 = CCUAACACUGUCUGGUAAAGAUGGCUCCCGGGU 193 miR-157 = GGGUUCUCUCGGCAGUAACCUUCAGGGAGCCCU overlap GAAGACCAUGGAGGAC miR-141 miR-158- GCCGAGACCGAGUGCACAGGGCUCUGACCUAUG 194 small = AAUUGACAGCCAGUGCUCUCGUCUCCCCUCUGGC miR-192 UGCCAAUUCCAUAGGUCACAGGUAUGUUCGCCU CAAUGCCAGC miR-159-1- UCCCGCCCCCUGUAACAGCAACUCCAUGUGGAAG 195 small UGCCCACUGGUUCCAGUGGGGCUGCUGUUAUCU GGGGCGAGGGCCA miR-161- AAAGCUGGGUUGAGAGGGCGAAAAAGGAUGAGG 196 small UGACUGGUCUGGGCUACGCUAUGCUGCGGCGCU CGGG miR-163- CAUUGGCCUCCUAAGCCAGGGAUUGUGGGUUCG 197 1b-small AGUCCCACCCGGGGUAAAGAAAGGCCGAAUU miR-163-3- CCUAAGCCAGGGAUUGUGGGUUCGAGUCCCACC 198 small UGGGGUAGAGGUGAAAGUUCCUUUUACGGAAUU UUUU miR-162 CAAUGUCAGCAGUGCCUUAGCAGCACGUAAAUA 199 UUGGCGUUAAGAUUCUAAAAUUAUCUCCAGUAU UAACUGUGCUGCUGAAGUAAGGUUGACCAUACU CUACAGUUG miR-175- GGGCUUUCAAGUCACUAGUGGUUCCGUUUAGUA 200 small = GAUGAUUGUGCAUUGUUUCAAAAUGGUGCCCUA miR-224 GUGACUACAAAGCCC miR-177- ACGCAAGUGUCCUAAGGUGAGCUCAGGGAGCAC 201 small AGAAACCUCCAGUGGAACAGAAGGGCAAAAGCU CAUU miR-180- CAUGUGUCACUUUCAGGUGGAGUUUCAAGAGUC 202 small CCUUCCUGGUUCACCGUCUCCUUUGCUCUUCCAC AAC miR-181a AGAAGGGCUAUCAGGCCAGCCUUCAGAGGACUC 203 CAAGGAACAUUCAACGCUGUCGGUGAGUUUGGG AUUUGAAAAAACCACUGACCGUUGACUGUACCU UGGGGUCCUUA miR-181b-1 CCUGUGCAGAGAUUAUUUUUUAAAAGGUCACAA 204 UCAACAUUCAUUGCUGUCGGUGGGUUGAACUGU GUGGACAAGCUCACUGAACAAUGAAUGCAACUG UGGCCCCGCUU miR-181b-2 CUGAUGGCUGCACUCAACAUUCAUUGCUGUCGG 205 UGGGUUUGAGUCUGAAUCAACUCACUGAUCAAU GAAUGCAAACUGCGGACCAAACA miR-181c CGGAAAAUUUGCCAAGGGUUUGGGGGAACAUUC 206 AACCUGUCGGUGAGUUUGGGCAGCUCAGGCAAA CCAUCGACCGUUGAGUGGACCCUGAGGCCUGGA AUUGCCAUCCU miR-182-as GAGCUGCUUGCCUCCCCCCGUUUUUGGCAAUGG 207 UAGAACUCACACUGGUGAGGUAACAGGAUCCGG UGGUUCUAGACUUGCCAACUAUGGGGCGAGGAC UCAGCCGGCAC miR-182 UUUUUGGCAAUGGUAGAACUCACACUGGUGAGG 208 UAACAGGAUCCGGUGGUUCUAGACUUGCCAACU AUGG miR-183 CCGCAGAGUGUGACUCCUGUUCUGUGUAUGGCA 209 CUGGUAGAAUUCACUGUGAACAGUCUCAGUCAG UGAAUUACCGAAGGGCCAUAAACAGAGCAGAGA CAGAUCCACGA miR-184-1 CCAGUCACGUCCCCUUAUCACUUUUCCAGCCCAG 210 CUUUGUGACUGUAAGUGUUGGACGGAGAACUGA UAAGGGUAGGUGAUUGA miR-184-2 CCUUAUCACUUUUCCAGCCCAGCUUUGUGACUG 211 UAAGUGUUGGACGGAGAACUGAUAAGGGUAGG miR-185-1 AGGGGGCGAGGGAUUGGAGAGAAAGGCAGUUCC 212 UGAUGGUCCCCUCCCCAGGGGCUGGCUUUCCUCU GGUCCUUCCCUCCCA miR-185-2 AGGGAUUGGAGAGAAAGGCAGUUCCUGAUGGUC 213 CCCUCCCCAGGGGCUGGCUUUCCUCUGGUCCUU miR-186-1 UGCUUGUAACUUUCCAAAGAAUUCUCCUUUUGG 214 GCUUUCUGGUUUUAUUUUAAGCCCAAAGGUGAA UUUUUUGGGAAGUUUGAGCU miR-186-2 ACUUUCCAAAGAAUUCUCCUUUUGGGCUUUCUG 215 GUUUUAUUUUAAGCCCAAAGGUGAAUUUUUUGG GAAGU miR-187 GGUCGGGCUCACCAUGACACAGUGUGAGACUCG 216 GGCUACAACACAGGACCCGGGGCGCUGCUCUGA CCCCUCGUGUCUUGUGUUGCAGCCGGAGGGACG CAGGUCCGCA miR-188-1 UGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAG 217 GGUGAGCUUUCUGAAAACCCCUCCCACAUGCAG GGUUUGCAGGAUGGCGAGCC miR-188-2 UCUCACAUCCCUUGCAUGGUGGAGGGUGAGCUU 218 UCUGAAAACCCCUCCCACAUGCAGGGUUUGCAG GA miR-189-1 CUGUCGAUUGGACCCGCCCUCCGGUGCCUACUGA 219 GCUGAUAUCAGUUCUCAUUUUACACACUGGCUC AGUUCAGCAGGAACAGGAGUCGAGCCCUUGAGC AA miR-189-2 CUCCGGUGCCUACUGAGCUGAUAUCAGUUCUCA 220 UUUUACACACUGGCUCAGUUCAGCAGGAACAGG AG miR-190-1 UGCAGGCCUCUGUGUGAUAUGUUUGAUAUAUUA 221 GGUUGUUAUUUAAUCCAACUAUAUAUCAAACAU AUUCCUACAGUGUCUUGCC miR-190-2 CUGUGUGAUAUGUUUGAUAUAUUAGGUUGUUAU 222 UUAAUCCAACUAUAUAUCAAACAUAUUCCUACA G miR-191-1 CGGCUGGACAGCGGGCAACGGAAUCCCAAAAGC 223 AGCUGUUGUCUCCAGAGCAUUCCAGCUGCGCUU GGAUUUCGUCCCCUGCUCUCCUGCCU miR-191-2 AGCGGGCAACGGAAUCCCAAAAGCAGCUGUUGU 224 CUCCAGAGCAUUCCAGCUGCGCUUGGAUUUCGU CCCCUGCU miR-192- CCGAGACCGAGUGCACAGGGCUCUGACCUAUGA 225 2/3 AUUGACAGCCAGUGCUCUCGUCUCCCCUCUGGCU GCCAAUUCCAUAGGUCACAGGUAUGUUCGCCUC AAUGCCAG miR-192 GCCGAGACCGAGUGCACAGGGCUCUGACCUAUG 226 AAUUGACAGCCAGUGCUCUCGUCUCCCCUCUGGC UGCCAAUUCCAUAGGUCACAGGUAUGUUCGCCU CAAUGCCAGC miR-193-1 CGAGGAUGGGAGCUGAGGGCUGGGUCUUUGCGG 227 GCGAGAUGAGGGUGUCGGAUCAACUGGCCUACA AAGUCCCAGUUCUCGGCCCCCG miR-193-2 GCUGGGUCUUUGCGGGCGAGAUGAGGGUGUCGG 228 AUCAACUGGCCUACAAAGUCCCAGU miR-194-1 AUGGUGUUAUCAAGUGUAACAGCAACUCCAUGU 229 GGACUGUGUACCAAUUUCCAGUGGAGAUGCUGU UACUUUUGAUGGUUACCAA miR-194-2 GUGUAACAGCAACUCCAUGUGGACUGUGUACCA 230 AUUUCCAGUGGAGAUGCUGUUACUUUUGAU miR-195-1 AGCUUCCCUGGCUCUAGCAGCACAGAAAUAUUG 231 GCACAGGGAAGCGAGUCUGCCAAUAUUGGCUGU GCUGCUCCAGGCAGGGUGGUG miR-195-2 UAGCAGCACAGAAAUAUUGGCACAGGGAAGCGA 232 GUCUGCCAAUAUUGGCUGUGCUGCU miR-196-1 CUAGAGCUUGAAUUGGAACUGCUGAGUGAAUUA 233 GGUAGUUUCAUGUUGUUGGGCCUGGGUUUCUGA ACACAACAACAUUAAACCACCCGAUUCACGGCA GUUACUGCUCC miR-196a-1 GUGAAUUAGGUAGUUUCAUGUUGUUGGGCCUGG 234 GUUUCUGAACACAACAACAUUAAACCACCCGAU UCAC miR-196a-2 UGCUCGCUCAGCUGAUCUGUGGCUUAGGUAGUU 235 (miR-196-2) UCAUGUUGUUGGGAUUGAGUUUUGAACUCGGCA ACAAGAAACUGCCUGAGUUACAUCAGUCGGUUU UCGUCGAGGGC miR-196 GUGAAUUAGGUAGUUUCAUGUUGUUGGGCCUGG 236 GUUUCUGAACACAACAACAUUAAACCACCCGAU UCAC miR-196b ACUGGUCGGUGAUUUAGGUAGUUUCCUGUUGUU 237 GGGAUCCACCUUUCUCUCGACAGCACGACACUGC CUUCAUUACUUCAGUUG miR-197 GGCUGUGCCGGGUAGAGAGGGCAGUGGGAGGUA 238 AGAGCUCUUCACCCUUCACCACCUUCUCCACCCA GCAUGGCC miR-197-2 GUGCAUGUGUAUGUAUGUGUGCAUGUGCAUGUG 239 UAUGUGUAUGAGUGCAUGCGUGUGUGC miR-198 UCAUUGGUCCAGAGGGGAGAUAGGUUCCUGUGA 240 UUUUUCCUUCUUCUCUAUAGAAUAAAUGA miR-199a-1 GCCAACCCAGUGUUCAGACUACCUGUUCAGGAG 241 GCUCUCAAUGUGUACAGUAGUCUGCACAUUGGU UAGGC miR-199a-2 AGGAAGCUUCUGGAGAUCCUGCUCCGUCGCCCC 242 AGUGUUCAGACUACCUGUUCAGGACAAUGCCGU UGUACAGUAGUCUGCACAUUGGUUAGACUGGGC AAGGGAGAGCA miR-199b CCAGAGGACACCUCCACUCCGUCUACCCAGUGUU 243 UAGACUAUCUGUUCAGGACUCCCAAAUUGUACA GUAGUCUGCACAUUGGUUAGGCUGGGCUGGGUU AGACCCUCGG miR-199s GCCAACCCAGUGUUCAGACUACCUGUUCAGGAG 244 GCUCUCAAUGUGUACAGUAGUCUGCACAUUGGU UAGGC miR-200a GCCGUGGCCAUCUUACUGGGCAGCAUUGGAUGG 245 AGUCAGGUCUCUAAUACUGCCUGGUAAUGAUGA CGGC miR-200b CCAGCUCGGGCAGCCGUGGCCAUCUUACUGGGC 246 AGCAUUGGAUGGAGUCAGGUCUCUAAUACUGCC UGGUAAUGAUGACGGCGGAGCCCUGCACG miR-200c CCCUCGUCUUACCCAGCAGUGUUUGGGUGCGGU 247 UGGGAGUCUCUAAUACUGCCGGGUAAUGAUGGA GG miR-202 GUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGG 248 AUCUGGCCUAAAGAGGUAUAGGGCAUGGGAAGA UGGAGC miR-203 GUGUUGGGGACUCGCGCGCUGGGUCCAGUGGUU 249 CUUAACAGUUCAACAGUUCUGUAGCGCAAUUGU GAAAUGUUUAGGACCACUAGACCCGGCGGGCGC GGCGACAGCGA miR-204 GGCUACAGUCUUUCUUCAUGUGACUCGUGGACU 250 UCCCUUUGUCAUCCUAUGCCUGAGAAUAUAUGA AGGAGGCUGGGAAGGCAAAGGGACGUUCAAUUG UCAUCACUGGC miR-205 AAAGAUCCUCAGACAAUCCAUGUGCUUCUCUUG 251 UCCUUCAUUCCACCGGAGUCUGUCUCAUACCCAA  CCAGAUUUCAGUGGAGUGAAGUUCAGGAGGCAU GGAGCUGACA miR-206-1 UGCUUCCCGAGGCCACAUGCUUCUUUAUAUCCCC 252 AUAUGGAUUACUUUGCUAUGGAAUGUAAGGAAG UGUGUGGUUUCGGCAAGUG miR-206-2 AGGCCACAUGCUUCUUUAUAUCCCCAUAUGGAU 253 UACUUUGCUAUGGAAUGUAAGGAAGUGUGUGGU UUU miR-208 UGACGGGCGAGCUUUUGGCCCGGGUUAUACCUG 254 AUGCUCACGUAUAAGACGAGCAAAAAGCUUGUU GGUCA miR-210 ACCCGGCAGUGCCUCCAGGCGCAGGGCAGCCCCU 255 GCCCACCGCACACUGCGCUGCCCCAGACCCACUG UGCGUGUGACAGCGGCUGAUCUGUGCCUGGGCA GCGCGACCC miR-211 UCACCUGGCCAUGUGACUUGUGGGCUUCCCUUU 256 GUCAUCCUUCGCCUAGGGCUCUGAGCAGGGCAG GGACAGCAAAGGGGUGCUCAGUUGUCACUUCCC ACAGCACGGAG miR-212 CGGGGCACCCCGCCCGGACAGCGCGCCGGCACCU 257 UGGCUCUAGACUGCUUACUGCCCGGGCCGCCCUC  AGUAACAGUCUCCAGUCACGGCCACCGACGCCUG GCCCCGCC miR-213-2 CCUGUGCAGAGAUUAUUUUUUAAAAGGUCACAA 258 UCAACAUUCAUUGCUGUCGGUGGGUUGAACUGU GUGGACAAGCUCACUGAACAAUGAAUGCAACUG UGGCCCCGCUU miR-213 GAGUUUUGAGGUUGCUUCAGUGAACAUUCAACG 259 CUGUCGGUGAGUUUGGAAUUAAAAUCAAAACCA UCGACCGUUGAUUGUACCCUAUGGCUAACCAUC AUCUACUCC miR-214 GGCCUGGCUGGACAGAGUUGUCAUGUGUCUGCC 260 UGUCUACACUUGCUGUGCAGAACAUCCGCUCAC CUGUACAGCAGGCACAGACAGGCAGUCACAUGA CAACCCAGCCU miR-215 AUCAUUCAGAAAUGGUAUACAGGAAAAUGACCU 261 AUGAAUUGACAGACAAUAUAGCUGAGUUUGUCU GUCAUUUCUUUAGGCCAAUAUUCUGUAUGACUG UGCUACUUCAA miR-216 GAUGGCUGUGAGUUGGCUUAAUCUCAGCUGGCA 262 ACUGUGAGAUGUUCAUACAAUCCCUCACAGUGG UCUCUGGGAUUAUGCUAAACAGAGCAAUUUCCU AGCCCUCACGA miR-217 AGUAUAAUUAUUACAUAGUUUUUGAUGUCGCAG 263 AUACUGCAUCAGGAACUGAUUGGAUAAGAAUCA GUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGC AUCUAAACAAG miR-218-1 GUGAUAAUGUAGCGAGAUUUUCUGUUGUGCUUG 264 AUCUAACCAUGUGGUUGCGAGGUAUGAGUAAAA CAUGGUUCCGUCAAGCACCAUGGAACGUCACGC AGCUUUCUACA miR-218-2 GACCAGUCGCUGCGGGGCUUUCCUUUGUGCUUG 265 AUCUAACCAUGUGGUGGAACGAUGGAAACGGAA CAUGGUUCUGUCAAGCACCGCGGAAAGCACCGU GCUCUCCUGCA miR-219 CCGCCCCGGGCCGCGGCUCCUGAUUGUCCAAACG 266 CAAUUCUCGAGUCUAUGGCUCCGGCCGAGAGUU GAGUCUGGACGUCCCGAGCCGCCGCCCCCAAACC UCGAGCGGG miR-219-1 CCGCCCCGGGCCGCGGCUCCUGAUUGUCCAAACG 267 CAAUUCUCGAGUCUAUGGCUCCGGCCGAGAGUU GAGUCUGGACGUCCCGAGCCGCCGCCCCCAAACC UCGAGCGGG miR-219-2 ACUCAGGGGCUUCGCCACUGAUUGUCCAAACGC 268 AAUUCUUGUACGAGUCUGCGGCCAACCGAGAAU UGUGGCUGGACAUCUGUGGCUGAGCUCCGGG miR-220 GACAGUGUGGCAUUGUAGGGCUCCACACCGUAU 269 CUGACACUUUGGGCGAGGGCACCAUGCUGAAGG UGUUCAUGAUGCGGUCUGGGAACUCCUCACGGA UCUUACUGAUG miR-221 UGAACAUCCAGGUCUGGGGCAUGAACCUGGCAU 270 ACAAUGUAGAUUUCUGUGUUCGUUAGGCAACAG CUACAUUGUCUGCUGGGUUUCAGGCUACCUGGA AACAUGUUCUC miR-222 GCUGCUGGAAGGUGUAGGUACCCUCAAUGGCUC 271 AGUAGCCAGUGUAGAUCCUGUCUUUCGUAAUCA GCAGCUACAUCUGGCUACUGGGUCUCUGAUGGC AUCUUCUAGCU miR-223 CCUGGCCUCCUGCAGUGCCACGCUCCGUGUAUUU 272 GACAAGCUGAGUUGGACACUCCAUGUGGUAGAG UGUCAGUUUGUCAAAUACCCCAAGUGCGGCACA UGCUUACCAG miR-224 GGGCUUUCAAGUCACUAGUGGUUCCGUUUAGUA 273 GAUGAUUGUGCAUUGUUUCAAAAUGGUGCCCUA GUGACUACAAAGCCC miR-294-1 CAAUCUUCCUUUAUCAUGGUAUUGAUUUUUCAG 274 (chr16) UGCUUCCCUUUUGUGUGAGAGAAGAUA miR-296 AGGACCCUUCCAGAGGGCCCCCCCUCAAUCCUGU 275 UGUGCCUAAUUCAGAGGGUUGGGUGGAGGCUCU CCUGAAGGGCUCU miR-299 AAGAAAUGGUUUACCGUCCCACAUACAUUUUGA 276 AUAUGUAUGUGGGAUGGUAAACCGCUUCUU miR-301 ACUGCUAACGAAUGCUCUGACUUUAUUGCACUA 277 CUGUACUUUACAGCUAGCAGUGCAAUAGUAUUG UCAAAGCAUCUGAAAGCAGG miR-302a CCACCACUUAAACGUGGAUGUACUUGCUUUGAA 278 ACUAAAGAAGUAAGUGCUUCCAUGUUUUGGUGA UGG miR-302b GCUCCCUUCAACUUUAACAUGGAAGUGCUUUCU 279 GUGACUUUAAAAGUAAGUGCUUCCAUGUUUUAG UAGGAGU miR-302c CCUUUGCUUUAACAUGGGGGUACCUGCUGUGUG 280 AAACAAAAGUAAGUGCUUCCAUGUUUCAGUGGA GG miR-302d CCUCUACUUUAACAUGGAGGCACUUGCUGUGAC 281 AUGACAAAAAUAAGUGCUUCCAUGUUUGAGUGU GG miR-320 GCUUCGCUCCCCUCCGCCUUCUCUUCCCGGUUCU 282 UCCCGGAGUCGGGAAAAGCUGGGUUGAGAGGGC GAAAAAGGAUGAGGU miR-321 UUGGCCUCCUAAGCCAGGGAUUGUGGGUUCGAG 283 UCCCACCCGGGGUAAAGAAAGGCCGA miR-323 UUGGUACUUGGAGAGAGGUGGUCCGUGGCGCGU 284 UCGCUUUAUUUAUGGCGCACAUUACACGGUCGA CCUCUUUGCAGUAUCUAAUC miR-324 CUGACUAUGCCUCCCCGCAUCCCCUAGGGCAUUG 285 GUGUAAAGCUGGAGACCCACUGCCCCAGGUGCU GCUGGGGGUUGUAGUC miR-325 AUACAGUGCUUGGUUCCUAGUAGGUGUCCAGUA 286 AGUGUUUGUGACAUAAUUUGUUUAUUGAGGACC UCCUAUCAAUCAAGCACUGUGCUAGGCUCUGG miR-326 CUCAUCUGUCUGUUGGGCUGGAGGCAGGGCCUU 287 UGUGAAGGCGGGUGGUGCUCAGAUCGCCUCUGG GCCCUUCCUCCAGCCCCGAGGCGGAUUCA miR-328 UGGAGUGGGGGGGCAGGAGGGGCUCAGGGAGAA 288 AGUGCAUACAGCCCCUGGCCCUCUCUGCCCUUCC GUCCCCUG miR-330 CUUUGGCGAUCACUGCCUCUCUGGGCCUGUGUC 289 UUAGGCUCUGCAAGAUCAACCGAGCAAAGCACA CGGCCUGCAGAGAGGCAGCGCUCUGCCC miR-331 GAGUUUGGUUUUGUUUGGGUUUGUUCUAGGUAU 290 GGUCCCAGGGAUCCCAGAUCAAACCAGGCCCCUG GGCCUAUCCUAGAACCAACCUAAGCUC miR-335 UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAA 291 AAUGUUUGUCAUAAACCGUUUUUCAUUAUUGCU CCUGACCUCCUCUCAUUUGCUAUAUUCA miR-337 GUAGUCAGUAGUUGGGGGGUGGGAACGGCUUCA 292 UACAGGAGUUGAUGCACAGUUAUCCAGCUCCUA UAUGAUGCCUUUCUUCAUCCCCUUCAA miR-338 UCUCCAACAAUAUCCUGGUGCUGAGUGAUGACU 293 CAGGCGACUCCAGCAUCAGUGAUUUUGUUGAAG A miR-339 CGGGGCGGCCGCUCUCCCUGUCCUCCAGGAGCUC 294 ACGUGUGCCUGCCUGUGAGCGCCUCGACGACAG AGCCGGCGCCUGCCCCAGUGUCUGCGC miR-340 UUGUACCUGGUGUGAUUAUAAAGCAAUGAGACU 295 GAUUGUCAUAUGUCGUUUGUGGGAUCCGUCUCA GUUACUUUAUAGCCAUACCUGGUAUCUUA miR-342 GAAACUGGGCUCAAGGUGAGGGGUGCUAUCUGU 296 GAUUGAGGGACAUGGUUAAUGGAAUUGUCUCAC ACAGAAAUCGCACCCGUCACCUUGGCCUACUUA miR-345 ACCCAAACCCUAGGUCUGCUGACUCCUAGUCCAG 297 GGCUCGUGAUGGCUGGUGGGCCCUGAACGAGGG GUCUGGAGGCCUGGGUUUGAAUAUCGACAGC miR-346 GUCUGUCUGCCCGCAUGCCUGCCUCUCUGUUGCU 298 CUGAAGGAGGCAGGGGCUGGGCCUGCAGCUGCC UGGGCAGAGCGGCUCCUGC miR-367 CCAUUACUGUUGCUAAUAUGCAACUCUGUUGAA 299 UAUAAAUUGGAAUUGCACUUUAGCAAUGGUGAU GG miR-368 AAAAGGUGGAUAUUCCUUCUAUGUUUAUGUUAU 300 UUAUGGUUAAACAUAGAGGAAAUUCCACGUUUU miR-369 UUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUU 301 AUUGACUUCGAAUAAUACAUGGUUGAUCUUUUC UCAG miR-370 AGACAGAGAAGCCAGGUCACGUCUCUGCAGUUA 302 CACAGCUCACGAGUGCCUGCUGGGGUGGAACCU GGUCUGUCU miR-371 GUGGCACUCAAACUGUGGGGGCACUUUCUGCUC 303 UCUGGUGAAAGUGCCGCCAUCUUUUGAGUGUUA C miR-372 GUGGGCCUCAAAUGUGGAGCACUAUUCUGAUGU 304 CCAAGUGGAAAGUGCUGCGACAUUUGAGCGUCA C miR-373 GGGAUACUCAAAAUGGGGGCGCUUUCCUUUUUG 305 UCUGUACUGGGAAGUGCUUCGAUUUUGGGGUGU CCC miR-374 UACAUCGGCCAUUAUAAUACAACCUGAUAAGUG 306 UUAUAGCACUUAUCAGAUUGUAUUGUAAUUGUC UGUGUA miR-hes1 AUGGAGCUGCUCACCCUGUGGGCCUCAAAUGUG 307 GAGGAACUAUUCUGAUGUCCAAGUGGAAAGUGC UGCGACAUUUGAGCGUCACCGGUGACGCCCAUA UCA miR-hes2 GCAUCCCCUCAGCCUGUGGCACUCAAACUGUGG 308 GGGCACUUUCUGCUCUCUGGUGAAAGUGCCGCC AUCUUUUGAGUGUUACCGCUUGAGAAGACUCAA CC miR-hes3 CGAGGAGCUCAUACUGGGAUACUCAAAAUGGGG 309 GCGCUUUCCUUUUUGUCUGUUACUGGGAAGUGC UUCGAUUUUGGGGUGUCCCUGUUUGAGUAGGGC AUC *An underlined sequence within a precursor sequence corresponds to a mature processed miR transcript (see Table 1b). Some precursor sequences have two underlined sequences denoting two different mature miRs that are derived from the same precursor. All sequences are human.

TABLE 1b Human Mature microRNA Sequences. Corresponding Mature Mature miRNA SEQ precursor miRNA Sequence ID microRNA(s); Name (5′ to 3′) NO. see Table 1a let-7a ugagguaguagguuguauaguu 310 let-7a-1;  let-7a-2; let-7a-3;  let-7a-4 let-7b ugagguaguagguugugugguu 311 let-7b let-7c ugagguaguagguuguaugguu 312 let-7c let-7d agagguaguagguugcauagu 313 let-7d;  let-7d-v1 let-7e ugagguaggagguuguauagu 314 let-7e let-7f ugagguaguagauuguauaguu 315 let-7f-1;  let-7f-2-1; let-7f-2-2 let-7g ugagguaguaguuuguacagu 316 let-7g let-7i ugagguaguaguuugugcu 317 let-7i miR-1 uggaauguaaagaaguaugua 318 miR-1b;  miR-1b-1; miR-1b-2 miR-7 uggaagacuagugauuuuguu 319 miR-7-1;  miR-7-1a; miR-7-2;  miR-7-3 miR-9 ucuuugguuaucuagcuguauga 320 miR-9-1;  miR-9-2; miR-9-3 miR-9* uaaagcuagauaaccgaaagu 321 miR-9-1;  miR-9-2; miR-9-3 miR-10a uacccuguagauccgaauuugug  322 miR-10a miR-10b uacccuguagaaccgaauuugu 323 miR-10b miR-15a uagcagcacauaaugguuugug 324 miR-15a;  miR-15a-2 miR-15b uagcagcacaucaugguuuaca 325 miR-15b miR-16 uagcagcacguaaauauuggcg 326 miR-16-1;  miR-16-2; miR-16-13 miR-17- caaagugcuuacagugcagguagu 327 miR-17 5p miR-17- acugcagugaaggcacuugu 328 miR-17 3p miR-18 uaaggugcaucuagugcagaua 329 miR-18;  miR-18-13 miR-19a ugugcaaaucuaugcaaaacuga  330 miR-19a;  miR-19a-13 miR-19b ugugcaaauccaugcaaaacuga  331 miR-19b-1;  miR-19b-2 miR-20 uaaagugcuuauagugcaggua 332 miR-20  (miR-20a) miR-21 uagcuuaucagacugauguuga 333 miR-21;  miR-21-17 miR-22 aagcugccaguugaagaacugu 334 miR-22 miR-23a aucacauugccagggauuucc 335 miR-23a miR-23b aucacauugccagggauuaccac  336 miR-23b miR-24 uggcucaguucagcaggaacag 337 miR-24-1;  miR-24-2; miR-24-19;  miR-24-9 miR-25 cauugcacuugucucggucuga 338 miR-25 miR-26a uucaaguaauccaggauaggcu 339 miR-26a;  miR-26a-1; miR-26a-2 miR-26b uucaaguaauucaggauaggu 340 miR-26b miR-27a uucacaguggcuaaguuccgcc 341 miR-27a miR-27b uucacaguggcuaaguucug 342 miR-27b-1;  miR-27b-2 miR-28 aaggagcucacagucuauugag 343 miR-28 miR-29a cuagcaccaucugaaaucgguu 344 miR-29a-2;  miR-29a miR-29b uagcaccauuugaaaucagu 345 miR-296-1;  miR-29b-2 miR-29c uagcaccauuugaaaucgguua 346 miR-29c miR-30a- uguaaacauccucgacuggaagc 347 miR-30a 5p miR-30a- cuuucagucggauguuugcagc 348 miR-30a 3p miR-30b uguaaacauccuacacucagc 349 miR-30b-1;  miR-30b-2 miR-30c uguaaacauccuacacucucagc  350 miR-30c miR-30d uguaaacauccccgacuggaag 351 miR-30d miR-30e uguaaacauccuugacugga 352 miR-30e miR-31 ggcaagaugcuggcauagcug 353 miR-31 miR-32 uauugcacauuacuaaguugc 354 miR-32 miR-33 gugcauuguaguugcauug 355 miR-33;  miR-33b miR-34a uggcagugucuuagcugguugu 356 miR-34a miR-34b aggcagugucauuagcugauug 357 miR-34b miR-34c aggcaguguaguuagcugauug 358 miR-34c miR-92 uauugcacuugucccggccugu 359 miR-92-2;  miR-92-1 miR-93 aaagugcuguucgugcagguag 360 miR-93-1;  miR-93-2 miR-95 uucaacggguauuuauugagca 361 miR-95 miR-96 uuuggcacuagcacauuuuugc 362 miR-96 miR-98 ugagguaguaaguuguauuguu 363 miR-98 miR-99a aacccguagauccgaucuugug 364 miR-99a miR-99b cacccguagaaccgaccuugcg 365 miR-99b miR-100 uacaguacugugauaacugaag 366 miR-100 miR-101 uacaguacugugauaacugaag 367 miR-101-1;  miR-101-2 miR-103 agcagcauuguacagggcuauga 368 miR-103-1 miR-105 ucaaaugcucagacuccugu 369 miR-105 miR-106- aaaagugcuuacagugcagguagc 370 miR-106-a a miR-106- uaaagugcugacagugcagau 371 miR-106-b b miR-107 agcagcauuguacagggcuauca 372 miR-107 miR-122a uggagugugacaaugguguuugu 373 miR-122a-1;  miR-122a-2 miR-124a uuaaggcacgcggugaaugcca 374 miR-124a-1;  miR-124a-2; miR-124a-3 miR-125a ucccugagacccuuuaaccugug 375 miR-125a-1;  miR-125a-2 miR-125b ucccugagacccuaacuuguga 376 miR-125b-1;  miR-125b-2 miR-126* cauuauuacuuuugguacgcg 377 miR-126-1;  miR-126-2 miR-126 ucguaccgugaguaauaaugc 378 miR-126-1;  miR-126-2 miR-127 ucggauccgucugagcuuggcu 379 miR-127-1;  miR-127-2 miR-128a ucacagugaaccggucucuuuu 380 miR-128;  miR-128a miR-128b ucacagugaaccggucucuuuc 381 miR-128b miR-129 cuuuuugcggucugggcuugc 382 miR-129-1;  miR-129-2 miR-130a cagugcaauguuaaaagggc 383 miR-130a miR-130b cagugcaaugaugaaagggcau 384 miR-130b miR-132 uaacagucuacagccauggucg 385 miR-132-1 miR-133a uugguccccuucaaccagcugu 386 miR-133a-1;  miR-133a-2 miR-133b uugguccccuucaaccagcua 387 miR-133b miR-134 ugugacugguugaccagaggg 388 miR-134-1;  miR-134-2 miR-135a uauggcuuuuuauuccuauguga 389 miR-135a;  miR-135a-2 (miR-135-2) miR-135b uauggcuuuucauuccuaugug 390 miR-135b miR-136 acuccauuuguuuugaugaugga 391 miR-136-1;  miR-136-2 miR-137 uauugcuuaagaauacgcguag 392 miR-137 miR-138 agcugguguugugaauc 393 miR-138-1;  miR-138-2 miR-139 ucuacagugcacgugucu 394 miR-139 miR-140 agugguuuuacccuaugguag 395 miR-140;  miR-140as; miR-140s miR-141 aacacugucugguaaagaugg 396 miR-141-1;  miR-141-2 miR-142- uguaguguuuccuacuuuaugga 397 miR-142 3p miR-142- cauaaaguagaaagcacuac 398 miR-142 5p miR-143 ugagaugaagcacuguagcuca 399 miR-143-1 miR-144 uacaguauagaugauguacuag 400 miR-144-1;  miR-144-2 miR-145 guccaguuuucccaggaaucccuu 401 miR-145-1;  miR-145-2 miR-146 ugagaacugaauuccauggguu 402 miR-146-1;  miR-146-2 miR-147 guguguggaaaugcuucugc 403 miR-147 miR-148a ucagugcacuacagaacuuugu 404 miR-148a  (miR-148) miR-148b ucagugcaucacagaacuuugu 405 miR-148b miR-149 ucuggcuccgugucuucacucc 406 miR-149 miR-150 ucucccaacccuuguaccagug 407 miR-150-1;  miR-150-2 miR-151 acuagacugaagcuccuugagg 408 miR-151 miR-152 ucagugcaugacagaacuugg 409 miR-152-1;  miR-152-2 miR-153 uugcauagucacaaaaguga 410 miR-153-1-1;  miR-153-1-2; miR-153-2-1; miR-153-2-2 miR-154 uagguuauccguguugccuucg 411 miR-154-1;  miR-154-2 miR-154* aaucauacacgguugaccuauu 412 miR-154-1;  miR-154-2 miR-155 uuaaugcuaaucgugauagggg 413 miR-155 miR-181a aacauucaacgcugucggugagu 414 miR-181a miR-181b aacauucauugcugucgguggguu 415 miR-181b-1;  miR-181b-2 miR-181c aacauucaaccugucggugagu 416 miR-181c miR-182 uuuggcaaugguagaacucaca 417 miR-182;  miR-182as miR-182* ugguucuagacuugccaacua 418 miR-182;  miR-182as miR-183 uauggcacugguagaauucacug 419 miR-183 miR-184 uggacggagaacugauaagggu 420 miR-184-1;  miR-184-2 miR-185 uggagagaaaggcaguuc 421 miR-185-1;  miR-185-2 miR-186 caaagaauucuccuuuugggcuu 422 miR-186-1;  miR-186-2 miR-187 ucgugucuuguguugcagccg 423 miR-187 miR-188 caucccuugcaugguggagggu 424 miR-188 miR-189 gugccuacugagcugauaucagu  425 miR-189-1;  miR-189-2 miR-190 ugauauguuugauauauuaggu 426 miR-190-1;  miR-190-2 miR-191 caacggaaucccaaaagcagcu 427 miR-191-1;  miR-191-2 miR-192 cugaccuaugaauugacagcc 428 miR-192 miR-193 aacuggccuacaaagucccag 429 miR-193-1;  miR-193-2 miR-194 uguaacagcaacuccaugugga 430 miR-194-1;  miR-194-2 miR-195 uagcagcacagaaauauuggc 431 miR-195-1;  miR-195-2 miR-196a uagguaguuucauguuguugg 432 miR-196a;  miR-196a-2 (miR196-2) miR-196b uagguaguuuccuguuguugg 433 miR-196b miR-197 uucaccaccuucuccacccagc 434 miR-197 miR-198 gguccagaggggagauagg 435 miR-198 miR-199a cccaguguucagacuaccuguuc 436 miR-199a-1;  miR-199a-2 miR- uacaguagucugcacauugguu 437 miR-199a-1;  199a* miR-199a-2; miR-199s;  miR-199b miR-199b cccaguguuuagacuaucuguuc 438 miR-199b miR-200a uaacacugucugguaacgaugu 439 miR-200a miR-200b cucuaauacugccugguaaugaug 440 miR-200b miR-200c aauacugccggguaaugaugga 441 miR-200c miR-202 agagguauagggcaugggaaga 442 miR-202 miR-203 gugaaauguuuaggaccacuag 443 miR-203 miR-204 uucccuuugucauccuaugccu 444 miR-204 miR-205 uccuucauuccaccggagucug 445 miR-205 miR-206 uggaauguaaggaagugugugg 446 miR-206-1;  miR-206-2 miR-208 auaagacgagcaaaaagcuugu 447 miR-208 miR-210 cugugcgugugacagcggcug 448 miR-210 miR-211 uucccuuugucauccuucgccu 449 miR-211 miR-212 uaacagucuccagucacggcc 450 miR-212 miR-213 accaucgaccguugauuguacc 451 miR-213 miR-214 acagcaggcacagacaggcag 452 miR-214 miR-215 augaccuaugaauugacagac 453 miR-215 miR-216 uaaucucagcuggcaacugug 454 miR-216 miR-217 uacugcaucaggaacugauuggau 455 miR-217 miR-218 uugugcuugaucuaaccaugu 456 miR-218-1;  miR-218-2 miR-219 ugauuguccaaacgcaauucu 457 miR-219;  miR-219-1; miR-219-2 miR-220 ccacaccguaucugacacuuu 458 miR-220 miR-221 agcuacauugucugcuggguuuc 459 miR-221 miR-222 agcuacaucuggcuacugggucuc 460 miR-222 miR-223 ugucaguuugucaaauacccc 461 miR-223 miR-224 caagucacuagugguuccguuua 462 miR-224 miR-296 agggcccccccucaauccugu 463 miR-296 miR-299 ugguuuaccgucccacauacau 464 miR-299 miR-301 cagugcaauaguauugucaaagc 465 miR-301 miR-302a uaagugcuuccauguuuugguga 466 miR-302a miR- acuuuaacauggaagugcuuucu 467 miR-302b 302b* miR-302b uaagugcuuccauguuuuaguag 468 miR-302b miR- uuuaacauggggguaccugcug 469 miR-302c 302c* miR-302c uaagugcuuccauguuucagugg 470 miR-302c miR-302d uaagugcuuccauguuugagugu 471 miR-302d miR-320 aaaagcuggguugagagggcgaa 472 miR-320 miR-321 uaagccagggauuguggguuc 473 miR-321 miR-323 gcacauuacacggucgaccucu 474 miR-323 miR-324- cgcauccccuagggcauuggugu 475 miR-324 5p miR-324- ccacugccccaggugcugcugg 476 miR-324 3p miR-325 ccuaguagguguccaguaagu 477 miR-325 miR-326 ccucugggcccuuccuccag 478 miR-326 miR-328 cuggcccucucugcccuuccgu 479 miR-328 miR-330 gcaaagcacacggccugcagaga 480 miR-330 miR-331 gccccugggccuauccuagaa 481 miR-331 miR-335 ucaagagcaauaacgaaaaaugu 482 miR-335 miR-337 uccagcuccuauaugaugccuuu 483 miR-337 miR-338 uccagcaucagugauuuuguuga 484 miR-338 miR-339 ucccuguccuccaggagcuca 485 miR-339 miR-340 uccgucucaguuacuuuauagcc 486 miR-340 miR-342 ucucacacagaaaucgcacccguc 487 miR-342 miR-345 ugcugacuccuaguccagggc 488 miR-345 miR-346 ugucugcccgcaugccugccucu 489 miR-346 miR-367 aauugcacuuuagcaaugguga 490 miR-367 miR-368 acauagaggaaauuccacguuu 491 miR-368 miR-369 aauaauacaugguugaucuuu 492 miR-369 miR-370 gccugcugggguggaaccugg 493 miR-370 miR-371 gugccgccaucuuuugagugu 494 miR-371 miR-372 aaagugcugcgacauuugagcgu 495 miR-372 miR-373* acucaaaaugggggcgcuuucc 496 miR-373 miR-373 gaagugcuucgauuuuggggugu 497 miR-373 miR-374 uuauaauacaaccugauaagug 498 miR-374

The present invention encompasses methods of diagnosing whether a subject has, or is at risk for developing, a solid cancer, comprising measuring the level of at least one miR gene product in a test sample from the subject and comparing the level of the miR gene product in the test sample to the level of a corresponding miR gene product in a control sample. As used herein, a “subject” can be any mammal that has, or is suspected of having, a solid cancer. In a preferred embodiment, the subject is a human who has, or is suspected of having, a solid cancer.

In one embodiment, the at least one miR gene product measured in the test sample is selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof. In a particular embodiment, the miR gene product is miR-21, miR-191 or miR-17-5p. In another embodiment, the miR gene product is not miR-15a or miR-16-1. In an additional embodiment, the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the miR gene product is not miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the miR gene product is not miR-15a, miR-16-1, miR-182, miR-181, miR-30, miR-15a, miR-16-1, miR-15b, miR-16-2, miR-195, miR-34, miR-153, miR-21, miR-217, miR-205, miR-204, miR-211, miR-143, miR-96, miR-103, miR-107, miR-129, miR-9, miR-137, miR-217, miR-186.

The solid cancer can be any cancer that arises from organs and solid tissues. Such cancers are typically associated with the formation and/or presence of tumor masses and can be carcinomas, sarcomas and lymphomas. Specific examples of solid cancers to be diagnosed by the methods of the invention include, but are not limited to, colon cancer, rectal cancer, stomach (gastric) cancer, pancreatic cancer, breast cancer, lung cancer, prostate cancer, bronchial cancer, testicular cancer, ovarian cancer, uterine cancer, penile cancer, melanoma and other skin cancers, liver cancer, esophogeal cancer, cancers of the oral cavity and pharynx (e.g., tongue cancer, mouth cancer), cancers of the digestive system (e.g., intestinal cancer, gall bladder cancer), bone and joint cancers, cancers of the endocrine system (e.g., thyroid cancer), brain cancer, eye cancer, cancers of the urinary system (e.g., kidney cancer, urinary bladder cancer), Hodgkin disease and non-Hodgkin lymphoma. In particular embodiments, the solid cancer is not one or more of breast cancer, lung cancer, prostate cancer, pancreatic cancer or gastrointestinal cancer.

In one embodiment, the solid cancer is breast cancer or lung cancer and the at least one miR gene product measured in the test sample is selected from the group consisting of miR-210, miR-213 and a combination thereof.

In a further embodiment, the solid cancer is colon cancer, stomach cancer, prostate cancer or pancreas cancer and the at least one miR gene product measured in the test sample is miR-218-2.

In a certain embodiment of the invention, the solid cancer is breast cancer and the at least one miR gene product measured in the test sample is selected from the group consisting of miR-125b-1, miR-125b-2, miR-145, miR-21 and combinations thereof. In a related embodiment, the solid cancer is breast cancer and the at least one miR gene product in the test sample is selected from the group consisting of miR-21, miR-29b-2, miR-146, miR-125b-2, miR-125b-1, miR-10b, miR-145, miR-181a, miR-140, miR-213, miR-29a prec, miR-181b-1, miR-199b, miR-29b-1, miR-130a, miR-155, let-7a-2, miR-205, miR-29c, miR-224, miR-100, miR-31, miR-30c, miR-17-5p, miR-210, miR-122a, miR-16-2 and combinations thereof. In a related embodiment, the solid cancer is breast cancer and the at least one miR gene product is not miR-15a or miR-16-1. In a further embodiment, the solid cancer is breast cancer and the at least one miR gene product is not miR-145, miR-21, miR-155, miR-10b, miR-125b-1, miR-125b-2, let7a-2, let7a-3, let-7d, miR-122a, miR-191, miR-206, miR-210, let-71, miR-009-1 (miR131-1), (miR-170), miR-102 (miR-29b), miR-123 (miR-126), miR-140-as, miR-125a, miR-194, miR-204, miR-213, let-7f-2, miR-101, miR-128b, miR-136, miR-143, miR-149, miR-191, miR-196-1, miR-196-2, miR-202, miR-103-1, or miR-30c. In another embodiment, the solid cancer is breast cancer and the miR gene product is not miR-21, miR-125b-1, let-7a-2, let-71, miR-100, let-7g, miR-31, miR-32a-1, miR-33b, miR-34a-2, miR-101-1, miR-135-1, miR-142 as, miR-142s, miR-144, miR-301, miR-29c, miR-30c, miR-106a, or miR-29b-1. In yet another embodiment, the solid cancer is breast cancer and the miR gene product is not miR-159-1 or miR-192. In an additional embodiment, the solid cancer is breast cancer and the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the solid cancer is breast cancer and the miR gene product is not miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the solid cancer is breast cancer and the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the solid cancer is breast cancer and the miR gene product is not miR-181b, miR-181c, miR-181d, miR-30, miR-15b, miR-16-2, miR-153-1, miR-217, miR-205, miR-204, miR-103, miR-107, miR-129-2, miR-9 or miR-137.

In another embodiment, the solid cancer is colon cancer and the at least one miR gene product in the test sample is selected from the group consisting of miR-24-1, miR-29b-2, miR-20a, miR-10a, miR-32, miR-203, miR-106a, miR-17-5p, miR-30c, miR-223, miR-126*, miR-128b, miR-21, miR-24-2, miR-99b prec, miR-155, miR-213, miR-150, miR-107, miR-191, miR-221, miR-9-3 and combinations thereof. In another embodiment, the solid cancer is colon cancer and the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the solid cancer is colon cancer and the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the solid cancer is colon cancer and the miR gene product is not miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the solid cancer is colon cancer and the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the solid cancer is colon cancer and the miR gene product is not miR-181b, miR-181c, miR-181d, miR-30, miR-15b, miR-16-2, miR-153-1, miR-217, miR-205, miR-204, miR-103, miR-107, miR-129-2, miR-9 or miR-137.

In yet another embodiment, the solid cancer is lung cancer and the miR gene product in the test sample is selected from the group consisting of miR-21, miR-205, miR-200b, miR-9-1, miR-210, miR-148, miR-141, miR-132, miR-215, miR-128b, let-7g, miR-16-2, miR-129-1/2 prec, miR-126*, miR-142-as, miR-30d, miR-30a-5p, miR-7-2, miR-199a-1, miR-127, miR-34a prec, miR-34a, miR-136, miR-202, miR-196-2, miR-199a-2, let-7a-2, miR-124a-1, miR-149, miR-17-5p, miR-196-1 prec, miR-10a, miR-99b prec, miR-196-1, miR-199b, miR-191, miR-195, miR-155 and combinations thereof. In a related embodiment, the solid cancer is lung cancer and the at least one miR gene product is not miR-15a or miR-16-1. In a further embodiment, the solid cancer is lung cancer and the at least one miR gene product is not miR-21, miR-191, miR-126*, miR-210, miR-155, miR-143, miR-205, miR-126, miR-30a-5p, miR-140, miR-214, miR-218-2, miR-145, miR-106a, miR-192, miR-203, miR-150, miR-220, miR-192, miR-224, miR-24-2, miR-212, miR-9, miR-17, miR-124a-1, miR-95, miR-198, miR-216, miR-219-1, miR-197, miR-125a, miR-26a-1, miR-146, miR-199b, let7a-2, miR-27b, miR-32, miR-29b-2, miR-33, miR-181c, miR-101-1, miR-124a-3, miR-125b-1 or let7f-1. In another embodiment, the solid cancer is lung cancer and the at least one miR gene product is not miR-21, miR-182, miR-181, miR-30, miR-15a, miR-143, miR-205, miR-96, miR-103, miR-107, miR-129, miR-137, miR-186, miR-15b, miR-16-2, miR-195, miR-34, miR-153, miR-217, miR-204, miR-211, miR-9, miR-217, let-7a-2 or miR-32. In a further embodiment, the solid cancer is lung cancer and the miR gene product is not let-7c, let-7g, miR-7-3, miR-210, miR-31, miR-34a-1, miR-a-2, miR-99a, miR-100, miR-125b-2, miR-132, miR-135-1, miR-195, miR-34, miR-123, miR-203. In another embodiment, the solid cancer is lung cancer and the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the solid cancer is lung cancer and the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the solid cancer is lung cancer and the miR gene product is not miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the solid cancer is lung cancer and the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the solid cancer is lung cancer and the miR gene product is not miR-181b, miR-181c, miR-181d, miR-30, miR-15b, miR-16-2, miR-153-1, miR-217, miR-205, miR-204, miR-103, miR-107, miR-129-2, miR-9 or miR-137.

In a further embodiment, the solid cancer is pancreatic cancer and the at least one miR gene product measured in the test sample is selected from the group consisting of miR-103-1, miR-103-2, miR-155, miR-204 and combinations thereof. In a related embodiment, the solid cancer is pancreatic cancer and the miR gene product in the test sample is selected from the group consisting of miR-103-2, miR-103-1, miR-24-2, miR-107, miR-100, miR-125b-2, miR-125b-1, miR-24-1, miR-191, miR-23a, miR-26a-1, miR-125a, miR-130a, miR-26b, miR-145, miR-221, miR-126*, miR-16-2, miR-146, miR-214, miR-99b, miR-128b, miR-155, miR-29b-2, miR-29a, miR-25, miR-16-1, miR-99a, miR-224, miR-30d, miR-92-2, miR-199a-1, miR-223, miR-29c, miR-30b, miR-129-1/2, miR-197, miR-17-5p, miR-30c, miR-7-1, miR-93-1, miR-140, miR-30a-5p, miR-132, miR-181b-1, miR-152 prec, miR-23b, miR-20a, miR-222, miR-27a, miR-92-1, miR-21, miR-129-1/2 prec, miR-150, miR-32, miR-106a, miR-29b-1 and combinations thereof. In one embodiment, the solid cancer is pancreatic cancer and the miR gene product is not miR-15a or miR-16-1. In another embodiment, the solid cancer is pancreatic cancer and the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the solid cancer is pancreatic cancer and the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the solid cancer is pancreatic cancer and the miR gene product is not miR-21, miR-301, miR-142 as, miR-1425, miR-194, miR-215, or miR-32. In another embodiment, the solid cancer is pancreatic cancer and the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the solid cancer is pancreatic cancer and the miR gene product is not miR-181b, miR-181c, miR-181d, miR-30, miR-15b, miR-16-2, miR-153-1, miR-217, miR-205, miR-204, miR-103, miR-107, miR-129-2, miR-9 or miR-137.

In another embodiment, the solid cancer is prostate cancer and the miR gene product in the test sample is selected from the group consisting of let-7d, miR-128a prec, miR-195, miR-203, let-7a-2 prec, miR-34a, miR-20a, miR-218-2, miR-29a, miR-25, miR-95, miR-197, miR-135-2, miR-187, miR-196-1, miR-148, miR-191, miR-21, let-71, miR-198, miR-199a-2, miR-30c, miR-17-5p, miR-92-2, miR-146, miR-181b-1 prec, miR-32, miR-206, miR-184 prec, miR-29a prec, miR-29b-2, miR-149, miR-181b-1, miR-196-1 prec, miR-93-1, miR-223, miR-16-1, miR-101-1, miR-124a-1, miR-26a-1, miR-214, miR-27a, miR-24-1, miR-106a, miR-199a-1 and combinations thereof. In a related embodiment, the solid cancer is prostate cancer and the miR gene product is not miR-15a or miR-16-1. In another embodiment, the solid cancer is prostate cancer and the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the solid cancer is prostate cancer and the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the solid cancer is prostate cancer and the miR gene product is not miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the solid cancer is prostate cancer and the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the solid cancer is prostate cancer and the miR gene product is not miR-181b, miR-181c, miR-181d, miR-30, miR-15b, miR-16-2, miR-153-1, miR-217, miR-205, miR-204, miR-103, miR-107, miR-129-2, miR-9 or miR-137.

In yet another embodiment, the solid cancer is stomach cancer and the miR gene product in the test sample is selected from the group consisting of miR-223, miR-21, miR-218-2, miR-103-2, miR-92-2, miR-25, miR-136, miR-191, miR-221, miR-125b-2, miR-103-1, miR-214, miR-222, miR-212 prec, miR-125b-1, miR-100, miR-107, miR-92-1, miR-96, miR-192, miR-23a, miR-215, miR-7-2, miR-138-2, miR-24-1, miR-99b, miR-33b, miR-24-2 and combinations thereof. In a related embodiment, the solid cancer is stomach cancer and the miR gene product is not miR-15a or miR-16-1. In another embodiment, the solid cancer is stomach cancer and the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the solid cancer is stomach cancer and the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the solid cancer is stomach cancer and the miR gene product is not miR-21, miR-301, miR-142as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the solid cancer is stomach cancer and the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the solid cancer is stomach cancer and the miR gene product is not miR-181b, miR-181c, miR-181d, miR-30, miR-15b, miR-16-2, miR-153-1, miR-217, miR-205, miR-204, miR-103, miR-107, miR-129-2, miR-9 or miR-137.

The level of at least one miR gene product can be measured in a biological sample (e.g., cells, tissues) obtained from the subject. For example, a tissue sample (e.g., from a tumor) can be removed from a subject suspected of having a solid cancer by conventional biopsy techniques. In another embodiment, a blood sample can be removed from the subject, and blood cells (e.g., white blood cells) can be isolated for DNA extraction by standard techniques. The blood or tissue sample is preferably obtained from the subject prior to initiation of radiotherapy, chemotherapy or other therapeutic treatment. A corresponding control tissue or blood sample can be obtained from unaffected tissues of the subject, from a normal human individual or population of normal individuals, or from cultured cells corresponding to the majority of cells in the subject's sample. The control tissue or blood sample is then processed along with the sample from the subject, so that the levels of miR gene product produced from a given miR gene in cells from the subject's sample can be compared to the corresponding miR gene product levels from cells of the control sample. A reference miR expression standard for the biological sample can also be used as a control.

An alteration (e.g., an increase or decrease) in the level of a miR gene product in the sample obtained from the subject, relative to the level of a corresponding miR gene product in a control sample, is indicative of the presence of a solid cancer in the subject. In one embodiment, the level of the at least one miR gene product in the test sample is greater than the level of the corresponding miR gene product in the control sample (i.e., expression of the miR gene product is “up-regulated”). As used herein, expression of a miR gene product is “up-regulated” when the amount of miR gene product in a cell or tissue sample from a subject is greater than the amount of the same gene product in a control cell or tissue sample. In another embodiment, the level of the at least one miR gene product in the test sample is less than the level of the corresponding miR gene product in the control sample (i.e., expression of the miR gene product is “down-regulated”). As used herein, expression of a miR gene is “down-regulated” when the amount of miR gene product produced from that gene in a cell or tissue sample from a subject is less than the amount produced from the same gene in a control cell or tissue sample. The relative miR gene expression in the control and normal samples can be determined with respect to one or more RNA expression standards. The standards can comprise, for example, a zero miR gene expression level, the miR gene expression level in a standard cell line, the miR gene expression level in unaffected tissues of the subject, or the average level of miR gene expression previously obtained for a population of normal human controls.

The level of a miR gene product in a sample can be measured using any technique that is suitable for detecting RNA expression levels in a biological sample. Suitable techniques (e.g., Northern blot analysis, RT-PCR, in situ hybridization) for determining RNA expression levels in a biological sample (e.g., cells, tissues) are well known to those of skill in the art. In a particular embodiment, the level of at least one miR gene product is detected using Northern blot analysis. For example, total cellular RNA can be purified from cells by homogenization in the presence of nucleic acid extraction buffer, followed by centrifugation. Nucleic acids are precipitated, and DNA is removed by treatment with DNase and precipitation. The RNA molecules are then separated by gel electrophoresis on agarose gels according to standard techniques, and transferred to nitrocellulose filters. The RNA is then immobilized on the filters by heating. Detection and quantification of specific RNA is accomplished using appropriately labeled DNA or RNA probes complementary to the RNA in question. See, for example, Molecular Cloning: A Laboratory Manual, J. Sambrook et al., eds., 2nd edition, Cold Spring Harbor Laboratory Press, 1989, Chapter 7, the entire disclosure of which is incorporated by reference.

Suitable probes for Northern blot hybridization of a given miR gene product can be produced from the nucleic acid sequences provided in Table 1a and Table 1b and include, but are not limited to, probes having at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or complete complementarity to a miR gene product of interest. Methods for preparation of labeled DNA and RNA probes, and the conditions for hybridization thereof to target nucleotide sequences, are described in Molecular Cloning: A Laboratory Manual, J. Sambrook et al., eds., 2nd edition, Cold Spring Harbor Laboratory Press, 1989, Chapters 10 and 11, the disclosures of which are incorporated herein by reference.

For example, the nucleic acid probe can be labeled with, e.g., a radionuclide, such as ³H, ³²P, ³³P, ¹⁴C, or ³⁵S; a heavy metal; a ligand capable of functioning as a specific binding pair member for a labeled ligand (e.g., biotin, avidin or an antibody); a fluorescent molecule; a chemiluminescent molecule; an enzyme or the like.

Probes can be labeled to high specific activity by either the nick translation method of Rigby et al. (1977), J. Mol. Biol. 113:237-251 or by the random priming method of Fienberg et al. (1983), Anal. Biochem. 132:6-13, the entire disclosures of which are incorporated herein by reference. The latter is the method of choice for synthesizing ³²P-labeled probes of high specific activity from single-stranded DNA or from RNA templates. For example, by replacing preexisting nucleotides with highly radioactive nucleotides according to the nick translation method, it is possible to prepare ³²P-labeled nucleic acid probes with a specific activity well in excess of 10⁸ cpm/microgram. Autoradiographic detection of hybridization can then be performed by exposing hybridized filters to photographic film. Densitometric scanning of the photographic films exposed by the hybridized filters provides an accurate measurement of miR gene transcript levels. Using another approach, miR gene transcript levels can be quantified by computerized imaging systems, such as the Molecular Dynamics 400-B 2D Phosphorimager available from Amersham Biosciences, Piscataway, N.J.

Where radionuclide labeling of DNA or RNA probes is not practical, the random-primer method can be used to incorporate an analogue, for example, the dTTP analogue 5-(N—(N-biotinyl-epsilon-aminocaproyl)-3-aminoallyl)deoxyuridine triphosphate, into the probe molecule. The biotinylated probe oligonucleotide can be detected by reaction with biotin-binding proteins, such as avidin, streptavidin, and antibodies (e.g., anti-biotin antibodies) coupled to fluorescent dyes or enzymes that produce color reactions.

In addition to Northern and other RNA hybridization techniques, determining the levels of RNA transcripts can be accomplished using the technique of in situ hybridization. This technique requires fewer cells than the Northern blotting technique, and involves depositing whole cells onto a microscope cover slip and probing the nucleic acid content of the cell with a solution containing radioactive or otherwise labeled nucleic acid (e.g., cDNA or RNA) probes. This technique is particularly well-suited for analyzing tissue biopsy samples from subjects. The practice of the in situ hybridization technique is described in more detail in U.S. Pat. No. 5,427,916, the entire disclosure of which is incorporated herein by reference. Suitable probes for in situ hybridization of a given miR gene product can be produced from the nucleic acid sequences provided in Table 1a and Table 1b, and include, but are not limited to, probes having at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or complete complementarity to a miR gene product of interest, as described above.

The relative number of miR gene transcripts in cells can also be determined by reverse transcription of miR gene transcripts, followed by amplification of the reverse-transcribed transcripts by polymerase chain reaction (RT-PCR). The levels of miR gene transcripts can be quantified in comparison with an internal standard, for example, the level of mRNA from a “housekeeping” gene present in the same sample. A suitable “housekeeping” gene for use as an internal standard includes, e.g., myosin or glyceraldehyde-3-phosphate dehydrogenase (G3PDH). Methods for performing quantitative and semi-quantitative RT-PCR, and variations thereof, are well known to those of skill in the art.

In some instances, it may be desirable to simultaneously determine the expression level of a plurality of different miR gene products in a sample. In other instances, it may be desirable to determine the expression level of the transcripts of all known miR genes correlated with a cancer. Assessing cancer-specific expression levels for hundreds of miR genes or gene products is time consuming and requires a large amount of total RNA (e.g., at least 20 μg for each Northern blot) and autoradiographic techniques that require radioactive isotopes.

To overcome these limitations, an oligolibrary, in microchip format (i.e., a microarray), may be constructed containing a set of oligonucleotide (e.g., oligodeoxynucleotides) probes that are specific for a set of miR genes. Using such a microarray, the expression level of multiple microRNAs in a biological sample can be determined by reverse transcribing the RNAs to generate a set of target oligodeoxynucleotides, and hybridizing them to probe the oligonucleotides on the microarray to generate a hybridization, or expression, profile. The hybridization profile of the test sample can then be compared to that of a control sample to determine which microRNAs have an altered expression level in solid cancer cells. As used herein, “probe oligonucleotide” or “probe oligodeoxynucleotide” refers to an oligonucleotide that is capable of hybridizing to a target oligonucleotide. “Target oligonucleotide” or “target oligodeoxynucleotide” refers to a molecule to be detected (e.g., via hybridization). By “miR-specific probe oligonucleotide” or “probe oligonucleotide specific for a miR” is meant a probe oligonucleotide that has a sequence selected to hybridize to a specific miR gene product, or to a reverse transcript of the specific miR gene product.

An “expression profile” or “hybridization profile” of a particular sample is essentially a fingerprint of the state of the sample; while two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is unique to the state of the cell. That is, normal tissue may be distinguished from cancerous (e.g., tumor) tissue, and within cancerous tissue, different prognosis states (for example, good or poor long term survival prospects) may be determined. By comparing expression profiles of solid cancer tissue in different states, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained. The identification of sequences that are differentially expressed in solid cancer tissue, as well as differential expression resulting in different prognostic outcomes, allows the use of this information in a number of ways. For example, a particular treatment regime may be evaluated (e.g., to determine whether a chemotherapeutic drug acts to improve the long-term prognosis in a particular patient). Similarly, diagnosis may be done or confirmed by comparing patient samples with known expression profiles. Furthermore, these gene expression profiles (or individual genes) allow screening of drug candidates that suppress the solid cancer expression profile or convert a poor prognosis profile to a better prognosis profile.

Accordingly, the invention provides methods of diagnosing whether a subject has, or is at risk for developing, a solid cancer, comprising reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides, hybridizing the target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample, and comparing the test sample hybridization profile to a hybridization profile generated from a control sample or reference standard, wherein an alteration in the signal of at least one miRNA is indicative of the subject either having, or being at risk for developing, a solid cancer. In one embodiment, the microarray comprises miRNA-specific probe oligonucleotides for a substantial portion of all known human miRNAs. In a particular embodiment, the microarray comprises miRNA-specific probe oligonucleotides for one or more miRNAs selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

The microarray can be prepared from gene-specific oligonucleotide probes generated from known miRNA sequences. The array may contain two different oligonucleotide probes for each miRNA, one containing the active, mature sequence and the other being specific for the precursor of the miRNA. The array may also contain controls, such as one or more mouse sequences differing from human orthologs by only a few bases, which can serve as controls for hybridization stringency conditions. tRNAs or other RNAs (e.g., rRNAs, mRNAs) from both species may also be printed on the microchip, providing an internal, relatively stable, positive control for specific hybridization. One or more appropriate controls for non-specific hybridization may also be included on the microchip. For this purpose, sequences are selected based upon the absence of any homology with any known miRNAs.

The microarray may be fabricated using techniques known in the art. For example, probe oligonucleotides of an appropriate length, e.g., 40 nucleotides, are 5′-amine modified at position C6 and printed using commercially available microarray systems, e.g., the GeneMachine OmniGrid™ 100 Microarrayer and Amersham CodeLink™ activated slides. Labeled cDNA oligomer corresponding to the target RNAs is prepared by reverse transcribing the target RNA with labeled primer. Following first strand synthesis, the RNA/DNA hybrids are denatured to degrade the RNA templates. The labeled target cDNAs thus prepared are then hybridized to the microarray chip under hybridizing conditions, e.g., 6×SSPE/30% formamide at 25° C. for 18 hours, followed by washing in 0.75×TNT (Tris HCl/NaCl/Tween 20) at 37° C. for 40 minutes. At positions on the array where the immobilized probe DNA recognizes a complementary target cDNA in the sample, hybridization occurs. The labeled target cDNA marks the exact position on the array where binding occurs, allowing automatic detection and quantification. The output consists of a list of hybridization events, indicating the relative abundance of specific cDNA sequences, and therefore the relative abundance of the corresponding complementary miRs, in the patient sample. According to one embodiment, the labeled cDNA oligomer is a biotin-labeled cDNA, prepared from a biotin-labeled primer. The microarray is then processed by direct detection of the biotin-containing transcripts using, e.g., Streptavidin-Alexa647 conjugate, and scanned utilizing conventional scanning methods. Image intensities of each spot on the array are proportional to the abundance of the corresponding miR in the patient sample.

The use of the array has several advantages for miRNA expression detection. First, the global expression of several hundred genes can be identified in the same sample at one time point. Second, through careful design of the oligonucleotide probes, expression of both mature and precursor molecules can be identified. Third, in comparison with Northern blot analysis, the chip requires a small amount of RNA, and provides reproducible results using 2.5 μg of total RNA. The relatively limited number of miRNAs (a few hundred per species) allows the construction of a common microarray for several species, with distinct oligonucleotide probes for each. Such a tool would allow for analysis of trans-species expression for each known miR under various conditions.

In addition to use for quantitative expression level assays of specific miRs, a microchip containing miRNA-specific probe oligonucleotides corresponding to a substantial portion of the miRNome, preferably the entire miRNome, may be employed to carry out miR gene expression profiling, for analysis of miR expression patterns. Distinct miR signatures can be associated with established disease markers, or directly with a disease state.

According to the expression profiling methods described herein, total RNA from a sample from a subject suspected of having a cancer (e.g., a solid cancer) is quantitatively reverse transcribed to provide a set of labeled target oligodeoxynucleotides complementary to the RNA in the sample. The target oligodeoxynucleotides are then hybridized to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the sample. The result is a hybridization profile for the sample representing the expression pattern of miRNA in the sample. The hybridization profile comprises the signal from the binding of the target oligodeoxynucleotides from the sample to the miRNA-specific probe oligonucleotides in the microarray. The profile may be recorded as the presence or absence of binding (signal vs. zero signal). More preferably, the profile recorded includes the intensity of the signal from each hybridization. The profile is compared to the hybridization profile generated from a normal, i.e., noncancerous, control sample. An alteration in the signal is indicative of the presence of, or propensity to develop, cancer in the subject.

Other techniques for measuring miR gene expression are also within the skill in the art, and include various techniques for measuring rates of RNA transcription and degradation.

The invention also provides methods of determining the prognosis of a subject with a solid cancer, comprising measuring the level of at least one miR gene product, which is associated with a particular prognosis in a solid cancer (e.g., a good or positive prognosis, a poor or adverse prognosis), in a test sample from the subject. According to these methods, an alteration in the level of a miR gene product that is associated with a particular prognosis in the test sample, as compared to the level of a corresponding miR gene product in a control sample, is indicative of the subject having a solid cancer with a particular prognosis. In one embodiment, the miR gene product is associated with an adverse (i.e., poor) prognosis. Examples of an adverse prognosis include, but are not limited to, low survival rate and rapid disease progression. In certain embodiments, the level of the at least one miR gene product is measured by reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides, hybridizing the target oligodeoxynucleotides to a microarray that comprises miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample, and comparing the test sample hybridization profile to a hybridization profile generated from a control sample.

Without wishing to be bound by any one theory, it is believed that alterations in the level of one or more miR gene products in cells can result in the deregulation of one or more intended targets for these miRs, which can lead to the formation of solid cancers. Therefore, altering the level of the miR gene product (e.g., by decreasing the level of a miR gene product that is up-regulated in solid cancer cells, by increasing the level of a miR gene product that is down-regulated in solid cancer cells) may successfully treat the solid cancer.

Accordingly, the present invention encompasses methods of inhibiting tumorigenesis in a subject who has, or is suspected of having, a solid cancer wherein at least one miR gene product is deregulated (e.g., down-regulated, up-regulated) in the cancer cells of the subject. When the at least one isolated miR gene product is down-regulated in the cancer cells (e.g., miR-145, miR-155, miR-218-2), the method comprises administering an effective amount of the at least one isolated miR gene product, or an isolated variant or biologically-active fragment thereof, such that proliferation of cancer cells in the subject is inhibited. In one embodiment, the isolated miR gene product that is administered is not miR-15a or miR-16-1. In another embodiment, the miR gene product is not miR 159-1 or miR-192. In an additional embodiment, the miR gene product is not miR-186, miR-101-1, miR-194, miR-215, miR-106b, miR-25, miR-93, miR-29b, miR-29a, miR-96, miR-182s, miR-182 as, miR-183, miR-129-1, let-7a-1, let-7d, let-7f-1, miR-23b, miR-24-1, miR-27b, miR-32, miR-159-1, miR-192, miR-125b-1, let-7a-2, miR-100, miR-196-2, miR-148b, miR-190, miR-21, miR-301, miR-142s, miR-142 as, miR-105-1, or miR-175. In a further embodiment, the miR gene product is not miR-21, miR-301, miR-142 as, miR-142s, miR-194, miR-215, or miR-32. In another embodiment, the miR gene product is not miR-148, miR-10a, miR-196-1, miR-152, miR-196-2, miR-148b, miR-10b, miR-129-1, miR-153-2, miR-202, miR-139, let-7a, let-7f, or let-7d. In yet another embodiment, the miR gene product is not miR-30, miR-15b, miR-16-2, miR-217, miR-205, miR-204, miR-103, miR-107, miR-9, and miR-137. In a further embodiment, the miR gene product is not miR-145, miR-21, miR-155, miR-10b, miR-125b-1, miR-125b-2, let7a-2, let7a-3, let-7d, miR-122a, miR-191, miR-206, miR-210, let-71, miR-009-1 (miR131-1), miR-34 (miR-170), miR-102 (miR-29b), miR-123 (miR-126), miR-140-as, miR-125a, miR-194, miR-204, miR-213, let-7f-2, miR-101, miR-128b, miR-136, miR-143, miR-149, miR-191, miR-196-1, miR-196-2, miR-202, miR-103-1, or miR-30c. In another embodiment, the miR gene product is not miR-21, miR-125b-1, let-7a-2, let-71, miR-100, let-7g, miR-31, miR-32a-1, miR-33b, miR-34a-2, miR-101-1, miR-135-1, miR-142 as, miR-142s, miR-144, miR-301, miR-29c, miR-30c, miR-106a, or miR-29b-1.

For example, when a miR gene product is down-regulated in a cancer cell in a subject, administering an effective amount of an isolated miR gene product to the subject can inhibit proliferation of the cancer cell. The isolated miR gene product that is administered to the subject can be identical to the endogenous wild-type miR gene product (e.g., a miR gene product shown in Table 1a or Table 1b) that is down-regulated in the cancer cell or it can be a variant or biologically-active fragment thereof. As defined herein, a “variant” of a miR gene product refers to a miRNA that has less than 100% identity to a corresponding wild-type miR gene product and possesses one or more biological activities of the corresponding wild-type miR gene product. Examples of such biological activities include, but are not limited to, inhibition of expression of a target RNA molecule (e.g., inhibiting translation of a target RNA molecule, modulating the stability of a target RNA molecule, inhibiting processing of a target RNA molecule) and inhibition of a cellular process associated with solid cancer (e.g., cell differentiation, cell growth, cell death). These variants include species variants and variants that are the consequence of one or more mutations (e.g., a substitution, a deletion, an insertion) in a miR gene. In certain embodiments, the variant is at least about 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to a corresponding wild-type miR gene product.

As defined herein, a “biologically-active fragment” of a miR gene product refers to an RNA fragment of a miR gene product that possesses one or more biological activities of a corresponding wild-type miR gene product. As described above, examples of such biological activities include, but are not limited to, inhibition of expression of a target RNA molecule and inhibition of a cellular process associated with solid cancer. In certain embodiments, the biologically-active fragment is at least about 5, 7, 10, 12, 15, or 17 nucleotides in length. In a particular embodiment, an isolated miR gene product can be administered to a subject in combination with one or more additional anti-cancer treatments. Suitable anti-cancer treatments include, but are not limited to, chemotherapy, radiation therapy and combinations thereof (e.g., chemoradiation).

When the at least one isolated miR gene product is up-regulated in the cancer cells, the method comprises administering to the subject an effective amount of at least one compound for inhibiting expression of the at least one miR gene product, referred to herein as miR gene expression-inhibition compounds, such that proliferation of solid cancer cells is inhibited. In a particular embodiment, the at least one miR expression-inhibition compound is specific for a miR gene product selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof. A miR gene expression-inhibiting compound can be administered to a subject in combination with one or more additional anti-cancer treatments. Suitable anti-cancer treatments include, but are not limited to, chemotherapy, radiation therapy and combinations thereof (e.g., chemoradiation).

The terms “treat”, “treating” and “treatment”, as used herein, refer to ameliorating symptoms associated with a disease or condition, for example, a solid cancer, including preventing or delaying the onset of the disease symptoms, and/or lessening the severity or frequency of symptoms of the disease or condition. The terms “subject”, “patient” and “individual” are defined herein to include animals, such as mammals, including, but not limited to, primates, cows, sheep, goats, horses, dogs, cats, rabbits, guinea pigs, rats, mice or other bovine, ovine, equine, canine, feline, rodent, or murine species. In a preferred embodiment, the animal is a human.

As used herein, an “effective amount” of an isolated miR gene product is an amount sufficient to inhibit proliferation of a cancer cell in a subject suffering from a solid cancer. One skilled in the art can readily determine an effective amount of a miR gene product to be administered to a given subject, by taking into account factors, such as the size and weight of the subject; the extent of disease penetration; the age, health and sex of the subject; the route of administration; and whether the administration is regional or systemic.

For example, an effective amount of an isolated miR gene product can be based on the approximate weight of a tumor mass to be treated. The approximate weight of a tumor mass can be determined by calculating the approximate volume of the mass, wherein one cubic centimeter of volume is roughly equivalent to one gram. An effective amount of the isolated miR gene product based on the weight of a tumor mass can be in the range of about 10-500 micrograms/gram of tumor mass. In certain embodiments, the tumor mass can be at least about 10 micrograms/gram of tumor mass, at least about 60 micrograms/gram of tumor mass or at least about 100 micrograms/gram of tumor mass.

An effective amount of an isolated miR gene product can also be based on the approximate or estimated body weight of a subject to be treated. Preferably, such effective amounts are administered parenterally or enterally, as described herein. For example, an effective amount of the isolated miR gene product is administered to a subject can range from about 5 3000 micrograms/kg of body weight, from about 700-1000 micrograms/kg of body weight, or greater than about 1000 micrograms/kg of body weight.

One skilled in the art can also readily determine an appropriate dosage regimen for the administration of an isolated miR gene product to a given subject. For example, a miR gene product can be administered to the subject once (e.g., as a single injection or deposition). Alternatively, a miR gene product can be administered once or twice daily to a subject for a period of from about three to about twenty-eight days, more particularly from about seven to about ten days. In a particular dosage regimen, a miR gene product is administered once a day for seven days. Where a dosage regimen comprises multiple administrations, it is understood that the effective amount of the miR gene product administered to the subject can comprise the total amount of gene product administered over the entire dosage regimen.

As used herein, an “isolated” miR gene product is one that is synthesized, or altered or removed from the natural state through human intervention. For example, a synthetic miR gene product, or a miR gene product partially or completely separated from the coexisting materials of its natural state, is considered to be “isolated.” An isolated miR gene product can exist in substantially-purified form, or can exist in a cell into which the miR gene product has been delivered. Thus, a miR gene product that is deliberately delivered to, or expressed in, a cell is considered an “isolated” miR gene product. A miR gene product produced inside a cell from a miR precursor molecule is also considered to be an “isolated” molecule. According to the invention, the isolated miR gene products described herein can be used for the manufacture of a medicament for treating a solid cancer in a subject (e.g., a human).

Isolated miR gene products can be obtained using a number of standard techniques. For example, the miR gene products can be chemically synthesized or recombinantly produced using methods known in the art. In one embodiment, miR gene products are chemically synthesized using appropriately protected ribonucleoside phosphoramidites and a conventional DNA/RNA synthesizer. Commercial suppliers of synthetic RNA molecules or synthesis reagents include, e.g., Proligo (Hamburg, Germany), Dharmacon Research (Lafayette, Colo., U.S.A.), Pierce Chemical (part of Perbio Science, Rockford, Ill., U.S.A.), Glen Research (Sterling, Va., U.S.A.), ChemGenes (Ashland, Mass., U.S.A.) and Cruachem (Glasgow, UK).

Alternatively, the miR gene products can be expressed from recombinant circular or linear DNA plasmids using any suitable promoter. Suitable promoters for expressing RNA from a plasmid include, e.g., the U6 or H1 RNA pol III promoter sequences, or the cytomegalovirus promoters. Selection of other suitable promoters is within the skill in the art. The recombinant plasmids of the invention can also comprise inducible or regulatable promoters for expression of the miR gene products in cancer cells.

The miR gene products that are expressed from recombinant plasmids can be isolated from cultured cell expression systems by standard techniques. The miR gene products that are expressed from recombinant plasmids can also be delivered to, and expressed directly in, the cancer cells. The use of recombinant plasmids to deliver the miR gene products to cancer cells is discussed in more detail below.

The miR gene products can be expressed from a separate recombinant plasmid, or they can be expressed from the same recombinant plasmid. In one embodiment, the miR gene products are expressed as RNA precursor molecules from a single plasmid, and the precursor molecules are processed into the functional miR gene product by a suitable processing system, including, but not limited to, processing systems extant within a cancer cell. Other suitable processing systems include, e.g., the in vitro Drosophila cell lysate system (e.g., as described in U.S. Published Patent Application No. 2002/0086356 to Tuschl et al., the entire disclosure of which is incorporated herein by reference) and the E. coli RNAse III system (e.g., as described in U.S. Published Patent Application No. 2004/0014113 to Yang et al., the entire disclosure of which is incorporated herein by reference).

Selection of plasmids suitable for expressing the miR gene products, methods for inserting nucleic acid sequences into the plasmid to express the gene products, and methods of delivering the recombinant plasmid to the cells of interest are within the skill in the art. See, for example, Zeng et al. (2002), Molecular Cell 9:1327-1333; Tuschl (2002), Nat. Biotechnol, 20:446-448; Brummelkamp et al. (2002), Science 296:550-553; Miyagishi et al. (2002), Nat. Biotechnol. 20:497-500; Paddison et al. (2002), Genes Dev. 16:948-958; Lee et al. (2002), Nat. Biotechnol. 20:500-505; and Paul et al. (2002), Nat. Biotechnol. 20:505-508, the entire disclosures of which are incorporated herein by reference.

In one embodiment, a plasmid expressing the miR gene products comprises a sequence encoding a miR precursor RNA under the control of the CMV intermediate-early promoter. As used herein, “under the control” of a promoter means that the nucleic acid sequences encoding the miR gene product are located 3′ of the promoter, so that the promoter can initiate transcription of the miR gene product coding sequences.

The miR gene products can also be expressed from recombinant viral vectors. It is contemplated that the miR gene products can be expressed from two separate recombinant viral vectors, or from the same viral vector. The RNA expressed from the recombinant viral vectors can either be isolated from cultured cell expression systems by standard techniques, or can be expressed directly in cancer cells. The use of recombinant viral vectors to deliver the miR gene products to cancer cells is discussed in more detail below.

The recombinant viral vectors of the invention comprise sequences encoding the miR gene products and any suitable promoter for expressing the RNA sequences. Suitable promoters include, but are not limited to, the U6 or H1 RNA pol III promoter sequences, or the cytomegalovirus promoters. Selection of other suitable promoters is within the skill in the art. The recombinant viral vectors of the invention can also comprise inducible or regulatable promoters for expression of the miR gene products in a cancer cell.

Any viral vector capable of accepting the coding sequences for the miR gene products can be used; for example, vectors derived from adenovirus (AV); adeno-associated virus (AAV); retroviruses (e.g., lentiviruses (LV), Rhabdoviruses, murine leukemia virus); herpes virus, and the like. The tropism of the viral vectors can be modified by pseudotyping the vectors with envelope proteins or other surface antigens from other viruses, or by substituting different viral capsid proteins, as appropriate.

For example, lentiviral vectors of the invention can be pseudotyped with surface proteins from vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the like. AAV vectors of the invention can be made to target different cells by engineering the vectors to express different capsid protein serotypes. For example, an AAV vector expressing a serotype 2 capsid on a serotype 2 genome is called AAV 2/2. This serotype 2 capsid gene in the AAV 2/2 vector can be replaced by a serotype 5 capsid gene to produce an AAV 2/5 vector. Techniques for constructing AAV vectors that express different capsid protein serotypes are within the skill in the art; see, e.g., Rabinowitz, J. E., et al. (2002), J. Virol. 76:791-801, the entire disclosure of which is incorporated herein by reference.

Selection of recombinant viral vectors suitable for use in the invention, methods for inserting nucleic acid sequences for expressing RNA into the vector, methods of delivering the viral vector to the cells of interest, and recovery of the expressed RNA products are within the skill in the art. See, for example, Dornburg (1995), Gene Therapy 2:301-310; Eglitis (1988), Biotechniques 6:608-614; Miller (1990), Hum. Gene Therapy 1:5-14; and Anderson (1998), Nature 392:25-30, the entire disclosures of which are incorporated herein by reference.

Particularly suitable viral vectors are those derived from AV and AAV. A suitable AV vector for expressing the miR gene products, a method for constructing the recombinant AV vector, and a method for delivering the vector into target cells, are described in Xia et al. (2002), Nat. Biotech. 20:1006-1010, the entire disclosure of which is incorporated herein by reference. Suitable AAV vectors for expressing the miR gene products, methods for constructing the recombinant AAV vector, and methods for delivering the vectors into target cells are described in Samulski et al. (1987), J. Virol. 61:3096-3101; Fisher et al. (1996), J. Virol., 70:520-532; Samulski et al. (1989), J. Virol. 63:3822-3826; U.S. Pat. No. 5,252,479; U.S. Pat. No. 5,139,941; International Patent Application No. WO 94/13788; and International Patent Application No. WO 93/24641, the entire disclosures of which are incorporated herein by reference. In one embodiment, the miR gene products are expressed from a single recombinant AAV vector comprising the CMV intermediate early promoter.

In a certain embodiment, a recombinant AAV viral vector of the invention comprises a nucleic acid sequence encoding a miR precursor RNA in operable connection with a polyT termination sequence under the control of a human U6 RNA promoter. As used herein, “in operable connection with a polyT termination sequence” means that the nucleic acid sequences encoding the sense or antisense strands are immediately adjacent to the polyT termination signal in the 5′ direction. During transcription of the miR sequences from the vector, the polyT termination signals act to terminate transcription.

In other embodiments of the treatment methods of the invention, an effective amount of at least one compound that inhibits miR expression can be administered to the subject. As used herein, “inhibiting miR expression” means that the production of the precursor and/or active, mature form of miR gene product after treatment is less than the amount produced prior to treatment. One skilled in the art can readily determine whether miR expression has been inhibited in a cancer cell, using, for example, the techniques for determining miR transcript level discussed above for the diagnostic method. Inhibition can occur at the level of gene expression (i.e., by inhibiting transcription of a miR gene encoding the miR gene product) or at the level of processing (e.g., by inhibiting processing of a miR precursor into a mature, active miR).

As used herein, an “effective amount” of a compound that inhibits miR expression is an amount sufficient to inhibit proliferation of a cancer cell in a subject suffering from a cancer (e.g., a solid cancer). One skilled in the art can readily determine an effective amount of a miR expression-inhibition compound to be administered to a given subject, by taking into account factors, such as the size and weight of the subject; the extent of disease penetration; the age, health and sex of the subject; the route of administration; and whether the administration is regional or systemic.

For example, an effective amount of the expression-inhibition compound can be based on the approximate weight of a tumor mass to be treated, as described herein. An effective amount of a compound that inhibits miR expression can also be based on the approximate or estimated body weight of a subject to be treated, as described herein.

One skilled in the art can also readily determine an appropriate dosage regimen for administering a compound that inhibits miR expression to a given subject.

Suitable compounds for inhibiting miR gene expression include double-stranded RNA (such as short- or small-interfering RNA or “siRNA”), antisense nucleic acids, and enzymatic RNA molecules, such as ribozymes. Each of these compounds can be targeted to a given miR gene product and interfere with the expression of (e.g., inhibit translation of, induce cleavage or destruction of) the target miR gene product.

For example, expression of a given miR gene can be inhibited by inducing RNA interference of the miR gene with an isolated double-stranded RNA (“dsRNA”) molecule which has at least 90%, for example at least 95%, at least 98%, at least 99%, or 100%, sequence homology with at least a portion of the miR gene product. In a particular embodiment, the dsRNA molecule is a “short or small interfering RNA” or “siRNA.”

siRNA useful in the present methods comprise short double-stranded RNA from about 17 nucleotides to about 29 nucleotides in length, preferably from about 19 to about 25 nucleotides in length. The siRNA comprise a sense RNA strand and a complementary antisense RNA strand annealed together by standard Watson-Crick base-pairing interactions (hereinafter “base-paired”). The sense strand comprises a nucleic acid sequence that is substantially identical to a nucleic acid sequence contained within the target miR gene product.

As used herein, a nucleic acid sequence in an siRNA which is “substantially identical” to a target sequence contained within the target mRNA is a nucleic acid sequence that is identical to the target sequence, or that differs from the target sequence by one or two nucleotides. The sense and antisense strands of the siRNA can comprise two complementary, single-stranded RNA molecules, or can comprise a single molecule in which two complementary portions are base-paired and are covalently linked by a single-stranded “hairpin” area.

The siRNA can also be altered RNA that differs from naturally-occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siRNA or to one or more internal nucleotides of the siRNA, or modifications that make the siRNA resistant to nuclease digestion, or the substitution of one or more nucleotides in the siRNA with deoxyribonucleotides.

One or both strands of the siRNA can also comprise a 3′ overhang. As used herein, a “3′ overhang” refers to at least one unpaired nucleotide extending from the 3′-end of a duplexed RNA strand. Thus, in certain embodiments, the siRNA comprises at least one 3′ overhang of from 1 to about 6 nucleotides (which includes ribonucleotides or deoxyribonucleotides) in length, from 1 to about 5 nucleotides in length, from 1 to about 4 nucleotides in length, or from about 2 to about 4 nucleotides in length. In a particular embodiment, the 3′ overhang is present on both strands of the siRNA, and is 2 nucleotides in length. For example, each strand of the siRNA can comprise 3′ overhangs of dithymidylic acid (“TT”) or diuridylic acid (“uu”).

The siRNA can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing dsRNA or siRNA molecules are described in U.S. Published Patent Application No. 2002/0173478 to Gewirtz and in U.S. Published Patent Application No. 2004/0018176 to Reich et al., the entire disclosures of both of which are incorporated herein by reference.

Expression of a given miR gene can also be inhibited by an antisense nucleic acid. As used herein, an “antisense nucleic acid” refers to a nucleic acid molecule that binds to target RNA by means of RNA-RNA, RNA-DNA or RNA-peptide nucleic acid interactions, which alters the activity of the target RNA. Antisense nucleic acids suitable for use in the present methods are single-stranded nucleic acids (e.g., RNA, DNA, RNA-DNA chimeras, peptide nucleic acid (PNA)) that generally comprise a nucleic acid sequence complementary to a contiguous nucleic acid sequence in a miR gene product. The antisense nucleic acid can comprise a nucleic acid sequence that is 50-100% complementary, 75-100% complementary, or 95-100% complementary to a contiguous nucleic acid sequence in a miR gene product. Nucleic acid sequences for the miR gene products are provided in Tables 1a and 1b. Without wishing to be bound by any theory, it is believed that the antisense nucleic acids activate RNase H or another cellular nuclease that digests the miR gene product/antisense nucleic acid duplex.

Antisense nucleic acids can also contain modifications to the nucleic acid backbone or to the sugar and base moieties (or their equivalent) to enhance target specificity, nuclease resistance, delivery or other properties related to efficacy of the molecule. Such modifications include cholesterol moieties, duplex intercalators, such as acridine, or one or more nuclease-resistant groups.

Antisense nucleic acids can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing are within the skill in the art; see, e.g., Stein and Cheng (1993), Science 261:1004 and U.S. Pat. No. 5,849,902 to Woolf et al., the entire disclosures of which are incorporated herein by reference.

Expression of a given miR gene can also be inhibited by an enzymatic nucleic acid. As used herein, an “enzymatic nucleic acid” refers to a nucleic acid comprising a substrate binding region that has complementarity to a contiguous nucleic acid sequence of a miR gene product, and which is able to specifically cleave the miR gene product. The enzymatic nucleic acid substrate binding region can be, for example, 50-100% complementary, 75-100% complementary, or 95-100% complementary to a contiguous nucleic acid sequence in a miR gene product. The enzymatic nucleic acids can also comprise modifications at the base, sugar, and/or phosphate groups. An exemplary enzymatic nucleic acid for use in the present methods is a ribozyme.

The enzymatic nucleic acids can be produced chemically or biologically, or can be expressed from a recombinant plasmid or viral vector, as described above for the isolated miR gene products. Exemplary methods for producing and testing dsRNA or siRNA molecules are described in Werner and Uhlenbeck (1995), Nucl. Acids Res. 23:2092-96; Hammann et al. (1999), Antisense and Nucleic Acid Drug Dev. 9:25-31; and U.S. Pat. No. 4,987,071 to Cech et al, the entire disclosures of which are incorporated herein by reference.

Administration of at least one miR gene product, or at least one compound for inhibiting miR expression, will inhibit the proliferation of cancer cells in a subject who has a solid cancer. As used herein, to “inhibit the proliferation of a cancer cell” means to kill the cell, or permanently or temporarily arrest or slow the growth of the cell. Inhibition of cancer cell proliferation can be inferred if the number of such cells in the subject remains constant or decreases after administration of the miR gene products or miR gene expression-inhibition compounds. An inhibition of cancer cell proliferation can also be inferred if the absolute number of such cells increases, but the rate of tumor growth decreases.

The number of cancer cells in the body of a subject can be determined by direct measurement, or by estimation from the size of primary or metastatic tumor masses. For example, the number of cancer cells in a subject can be measured by immunohistological methods, flow cytometry, or other techniques designed to detect characteristic surface markers of cancer cells.

The size of a tumor mass can be ascertained by direct visual observation, or by diagnostic imaging methods, such as X-ray, magnetic resonance imaging, ultrasound, and scintigraphy. Diagnostic imaging methods used to ascertain size of the tumor mass can be employed with or without contrast agents, as is known in the art. The size of a tumor mass can also be ascertained by physical means, such as palpation of the tissue mass or measurement of the tissue mass with a measuring instrument, such as a caliper.

The miR gene products or miR gene expression-inhibition compounds can be administered to a subject by any means suitable for delivering these compounds to cancer cells of the subject. For example, the miR gene products or miR expression-inhibition compounds can be administered by methods suitable to transfect cells of the subject with these compounds, or with nucleic acids comprising sequences encoding these compounds. In one embodiment, the cells are transfected with a plasmid or viral vector comprising sequences encoding at least one miR gene product or miR gene expression-inhibition compound.

Transfection methods for eukaryotic cells are well known in the art, and include, e.g., direct injection of the nucleic acid into the nucleus or pronucleus of a cell; electroporation; liposome transfer or transfer mediated by lipophilic materials; receptor-mediated nucleic acid delivery, bioballistic or particle acceleration; calcium phosphate precipitation, and transfection mediated by viral vectors.

For example, cells can be transfected with a liposomal transfer compound, e.g., DOTAP (N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethyl-ammonium methylsulfate, Boehringer-Mannheim) or an equivalent, such as LIPOFECTIN. The amount of nucleic acid used is not critical to the practice of the invention; acceptable results may be achieved with 0.1-100 micrograms of nucleic acid/10⁵ cells. For example, a ratio of about 0.5 micrograms of plasmid vector in 3 micrograms of DOTAP per 10⁵ cells can be used.

A miR gene product or miR gene expression-inhibition compound can also be administered to a subject by any suitable enteral or parenteral administration route. Suitable enteral administration routes for the present methods include, e.g., oral, rectal, or intranasal delivery. Suitable parenteral administration routes include, e.g., intravascular administration (e.g., intravenous bolus injection, intravenous infusion, intra-arterial bolus injection, intra-arterial infusion and catheter instillation into the vasculature); peri- and intra-tissue injection (e.g., peri-tumoral and intra-tumoral injection, intra-retinal injection, or subretinal injection); subcutaneous injection or deposition, including subcutaneous infusion (such as by osmotic pumps); direct application to the tissue of interest, for example by a catheter or other placement device (e.g., a retinal pellet or a suppository or an implant comprising a porous, non-porous, or gelatinous material); and inhalation. Particularly suitable administration routes are injection, infusion and direct injection into the tumor.

In the present methods, a miR gene product or miR gene product expression-inhibition compound can be administered to the subject either as naked RNA, in combination with a delivery reagent, or as a nucleic acid (e.g., a recombinant plasmid or viral vector) comprising sequences that express the miR gene product or miR gene product expression-inhibition compound. Suitable delivery reagents include, e.g., the Mirus Transit TKO lipophilic reagent; lipofectin; lipofectamine; cellfectin; polycations (e.g., polylysine), and liposomes.

Recombinant plasmids and viral vectors comprising sequences that express the miR gene products or miR gene expression-inhibition compounds, and techniques for delivering such plasmids and vectors to cancer cells, are discussed herein and/or are well known in the art.

In a particular embodiment, liposomes are used to deliver a miR gene product or miR gene expression-inhibition compound (or nucleic acids comprising sequences encoding them) to a subject. Liposomes can also increase the blood half-life of the gene products or nucleic acids. Suitable liposomes for use in the invention can be formed from standard vesicle-forming lipids, which generally include neutral or negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of factors, such as the desired liposome size and half-life of the liposomes in the blood stream. A variety of methods are known for preparing liposomes, for example, as described in Szoka et al. (1980), Ann. Rev. Biophys. Bioeng. 9:467; and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369, the entire disclosures of which are incorporated herein by reference.

The liposomes for use in the present methods can comprise a ligand molecule that targets the liposome to cancer cells. Ligands that bind to receptors prevalent in cancer cells, such as monoclonal antibodies that bind to tumor cell antigens, are preferred.

The liposomes for use in the present methods can also be modified so as to avoid clearance by the mononuclear macrophage system (“MMS”) and reticuloendothelial system (“RES”). Such modified liposomes have opsonization-inhibition moieties on the surface or incorporated into the liposome structure. In a particularly preferred embodiment, a liposome of the invention can comprise both an opsonization-inhibition moiety and a ligand.

Opsonization-inhibiting moieties for use in preparing the liposomes of the invention are typically large hydrophilic polymers that are bound to the liposome membrane. As used herein, an opsonization-inhibiting moiety is “bound” to a liposome membrane when it is chemically or physically attached to the membrane, e.g., by the intercalation of a lipid-soluble anchor into the membrane itself, or by binding directly to active groups of membrane lipids. These opsonization-inhibiting hydrophilic polymers form a protective surface layer that significantly decreases the uptake of the liposomes by the MMS and RES; e.g., as described in U.S. Pat. No. 4,920,016, the entire disclosure of which is incorporated herein by reference.

Opsonization-inhibiting moieties suitable for modifying liposomes are preferably water-soluble polymers with a number-average molecular weight from about 500 to about 40,000 daltons, and more preferably from about 2,000 to about 20,000 daltons. Such polymers include polyethylene glycol (PEG) or polypropylene glycol (PPG) derivatives; e.g., methoxy PEG or PPG, and PEG or PPG stearate; synthetic polymers, such as polyacrylamide or poly N-vinyl pyrrolidone; linear, branched, or dendrimeric polyamidoamines; polyacrylic acids; polyalcohols, e.g., polyvinylalcohol and polyxylitol to which carboxylic or amino groups are chemically linked, as well as gangliosides, such as ganglioside GM1. Copolymers of PEG, methoxy PEG, or methoxy PPG, or derivatives thereof, are also suitable. In addition, the opsonization-inhibiting polymer can be a block copolymer of PEG and either a polyamino acid, polysaccharide, polyamidoamine, polyethyleneamine, or polynucleotide. The opsonization-inhibiting polymers can also be natural polysaccharides containing amino acids or carboxylic acids, e.g., galacturonic acid, glucuronic acid, mannuronic acid, hyaluronic acid, pectic acid, neuraminic acid, alginic acid, carrageenan; aminated polysaccharides or oligosaccharides (linear or branched); or carboxylated polysaccharides or oligosaccharides, e.g., reacted with derivatives of carbonic acids with resultant linking of carboxylic groups. Preferably, the opsonization-inhibiting moiety is a PEG, PPG, or a derivative thereof. Liposomes modified with PEG or PEG-derivatives are sometimes called “PEGylated liposomes.”

The opsonization-inhibiting moiety can be bound to the liposome membrane by any one of numerous well-known techniques. For example, an N-hydroxysuccinimide ester of PEG can be bound to a phosphatidyl-ethanolamine lipid-soluble anchor, and then bound to a membrane. Similarly, a dextran polymer can be derivatized with a stearylamine lipid-soluble anchor via reductive amination using Na(CN)BH₃ and a solvent mixture, such as tetrahydrofuran and water in a 30:12 ratio at 60° C.

Liposomes modified with opsonization-inhibition moieties remain in the circulation much longer than unmodified liposomes. For this reason, such liposomes are sometimes called “stealth” liposomes. Stealth liposomes are known to accumulate in tissues fed by porous or “leaky” microvasculature. Thus, tissue characterized by such microvasculature defects, for example, solid tumors, will efficiently accumulate these liposomes; see Gabizon, et al. (1988), Proc. Natl. Acad. Sci., U.S.A., 18:6949-53. In addition, the reduced uptake by the RES lowers the toxicity of stealth liposomes by preventing significant accumulation of the liposomes in the liver and spleen. Thus, liposomes that are modified with opsonization-inhibition moieties are particularly suited to deliver the miR gene products or miR gene expression-inhibition compounds (or nucleic acids comprising sequences encoding them) to tumor cells.

The miR gene products or miR gene expression-inhibition compounds can be formulated as pharmaceutical compositions, sometimes called “medicaments,” prior to administering them to a subject, according to techniques known in the art. Accordingly, the invention encompasses pharmaceutical compositions for treating a solid cancer. In one embodiment, the pharmaceutical composition comprises at least one isolated miR gene product, or an isolated variant or biologically-active fragment thereof, and a pharmaceutically-acceptable carrier. In a particular embodiment, the at least one miR gene product corresponds to a miR gene product that has a decreased level of expression in solid cancer cells relative to suitable control cells. In certain embodiments the isolated miR gene product is selected from the group consisting of miR-145, miR-155, miR-218-2 combinations thereof.

In other embodiments, the pharmaceutical compositions of the invention comprise at least one miR expression-inhibition compound. In a particular embodiment, the at least one miR gene expression-inhibition compound is specific for a miR gene whose expression is greater in solid cancer cells than control cells. In certain embodiments, the miR gene expression-inhibition compound is specific for one or more miR gene products selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a and combinations thereof.

Pharmaceutical compositions of the present invention are characterized as being at least sterile and pyrogen-free. As used herein, “pharmaceutical compositions” include formulations for human and veterinary use. Methods for preparing pharmaceutical compositions of the invention are within the skill in the art, for example as described in Remington's Pharmaceutical Science, 17th ed., Mack Publishing Company, Easton, Pa. (1985), the entire disclosure of which is incorporated herein by reference.

The present pharmaceutical compositions comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) (e.g., 0.1 to 90% by weight), or a physiologically-acceptable salt thereof, mixed with a pharmaceutically-acceptable carrier. In certain embodiments, the pharmaceutical compositions of the invention additionally comprise one or more anti-cancer agents (e.g., chemotherapeutic agents). The pharmaceutical formulations of the invention can also comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them), which are encapsulated by liposomes and a pharmaceutically-acceptable carrier. In one embodiment, the pharmaceutical composition comprises a miR gene or gene product that is not miR-15 and/or miR-16.

Especially suitable pharmaceutically-acceptable carriers are water, buffered water, normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid and the like.

In a particular embodiment, the pharmaceutical compositions of the invention comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) that is resistant to degradation by nucleases. One skilled in the art can readily synthesize nucleic acids that are nuclease resistant, for example, by incorporating one or more ribonucleotides that is modified at the 2′-position into the miR gene product. Suitable 2′-modified ribonucleotides include those modified at the 2′-position with fluoro, amino, alkyl, alkoxy, and O-allyl.

Pharmaceutical compositions of the invention can also comprise conventional pharmaceutical excipients and/or additives. Suitable pharmaceutical excipients include stabilizers, antioxidants, osmolality adjusting agents, buffers, and pH adjusting agents. Suitable additives include, e.g., physiologically biocompatible buffers (e.g., tromethamine hydrochloride), additions of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (such as, for example, calcium DTPA, CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate). Pharmaceutical compositions of the invention can be packaged for use in liquid form, or can be lyophilized.

For solid pharmaceutical compositions of the invention, conventional nontoxic solid pharmaceutically-acceptable carriers can be used; for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.

For example, a solid pharmaceutical composition for oral administration can comprise any of the carriers and excipients listed above and 10-95%, preferably 25%-75%, of the at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them). A pharmaceutical composition for aerosol (inhalational) administration can comprise 0.01-20% by weight, preferably 1%-10% by weight, of the at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) encapsulated in a liposome as described above, and a propellant. A carrier can also be included as desired; e.g., lecithin for intranasal delivery.

The pharmaceutical compositions of the invention can further comprise one or more anti-cancer agents. In a particular embodiment, the compositions comprise at least one miR gene product or miR gene expression-inhibition compound (or at least one nucleic acid comprising sequences encoding them) and at least one chemotherapeutic agent. Chemotherapeutic agents that are suitable for the methods of the invention include, but are not limited to, DNA-alkylating agents, anti-tumor antibiotic agents, anti-metabolic agents, tubulin stabilizing agents, tubulin destabilizing agents, hormone antagonist agents, topoisomerase inhibitors, protein kinase inhibitors, HMG-CoA inhibitors, CDK inhibitors, cyclin inhibitors, caspase inhibitors, metalloproteinase inhibitors, antisense nucleic acids, triple-helix DNAs, nucleic acids aptamers, and molecularly-modified viral, bacterial and exotoxic agents. Examples of suitable agents for the compositions of the present invention include, but are not limited to, cytidine arabinoside, methotrexate, vincristine, etoposide (VP-16), doxorubicin (adriamycin), cisplatin (CDDP), dexamethasone, arglabin, cyclophosphamide, sarcolysin, methylnitrosourea, fluorouracil, 5-fluorouracil (5FU), vinblastine, camptothecin, actinomycin-D, mitomycin C, hydrogen peroxide, oxaliplatin, irinotecan, topotecan, leucovorin, carmustine, streptozocin, CPT-11, taxol, tamoxifen, dacarbazine, rituximab, daunorubicin, 1-β-D-arabinofuranosylcytosine, imatinib, fludarabine, docetaxel, FOLFOX4.

The invention also encompasses methods of identifying an inhibitor of tumorigenesis, comprising providing a test agent to a cell and measuring the level of at least one miR gene product in the cell. In one embodiment, the method comprises providing a test agent to a cell and measuring the level of at least one miR gene product associated with decreased expression levels in cancer cells. An increase in the level of the miR gene product in the cell after the agent is provided, relative to a suitable control cell (e.g., agent is not provided), is indicative of the test agent being an inhibitor of tumorigenesis. In a particular embodiment, at least one miR gene product associated with decreased expression levels in cancer cells is selected from the group consisting of miR-145, miR-155, miR-218-2 and combinations thereof.

In other embodiments the method comprises providing a test agent to a cell and measuring the level of at least one miR gene product associated with increased expression levels in cancer cells. A decrease in the level of the miR gene product in the cell after the agent is provided, relative to a suitable control cell (e.g., agent is not provided), is indicative of the test agent being an inhibitor of tumorigenesis. In a particular embodiment, at least one miR gene product associated with increased expression levels in cancer cells is selected from the group consisting of miR-21, miR-17-5p, miR-191, miR-29b-2, miR-223, miR-128b, miR-199a-1, miR-24-1, miR-24-2, miR-146, miR-155, miR-181b-1, miR-20a, miR-107, miR-32, miR-92-2, miR-214, miR-30c, miR-25, miR-221, miR-106a.

Suitable agents include, but are not limited to drugs (e.g., small molecules, peptides), and biological macromolecules (e.g., proteins, nucleic acids). The agent can be produced recombinantly, synthetically, or it may be isolated (i.e., purified) from a natural source. Various methods for providing such agents to a cell (e.g., transfection) are well known in the art, and several of such methods are described hereinabove. Methods for detecting the expression of at least one miR gene product (e.g., Northern blotting, in situ hybridization, RT-PCR, expression profiling) are also well known in the art. Several of these methods are also described hereinabove.

The invention will now be illustrated by the following non-limiting examples.

EXEMPLIFICATION

The following Materials and Methods were used in the Examples:

Samples

A total of 540 samples, including 363 primary tumor samples and 177 normal tissues, were used in this study (Table 2). The following solid cancers were represented: lung carcinoma, breast carcinoma, prostate carcinoma, stomach carcinoma, colon carcinoma and pancreatic endocrine tumors. All samples were obtained with informed consent from each patient and were confirmed histologically. Normal samples were paired with samples from individuals affected with lung and stomach carcinoma, and from normal individuals for the remaining tissues. All normal breast samples were obtained by pooling 5 unrelated normal tissues. Total RNA was isolated from tissues using TRIzol™ reagent (Invitrogen), according to manufacturer's instructions.

MicroRNA Microarrays.

Microarray analysis was performed as previously described (Liu, C.-G., et al., Proc. Natl. Acad. Sci. USA 101: 11755-11760 (2004)). Briefly, 5 μg of total RNA was used for hybridization on miRNA microarray chips. These chips contain gene-specific 40-mer oligonucleotide probes, spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6×SSPE (0.9 M NaCl/60 mM NaH₂PO₄.H₂O/8 mM EDTA, pH 7.4)/30% formamide at 25° C. for 18 hr, washed in 0.75×TNT (Tris.HCl/NaCl/Tween 20) at 37° C. for 40 min, and processed using direct detection of the biotin-labeled transcripts by streptavidin-Alexa647 (Molecular Probes) conjugate. Processed slides were scanned using a microarray scanner (GenePix Pro, Axon), with the laser set to 635 nm, at fixed PMT setting and a scan resolution of 10 mm. The data were confirmed by Northern blotting as described (Calin, G. A., et al., Proc. Natl. Acad. Sci. USA 101:11755-11760 (2004); Iorio, M. V., et al., Cancer Res. 65: 7065-7070 (2005)).

TABLE 2 Samples used in the study (tumors and corresponding normals). Tumour type Cancer Samples Normal Samples Lung carcinoma 123 123  Breast carcinoma 79  6* Colon carcinoma 46  8 Gastric carcinoma 20 21 Endocrine pancreatic tumours 39 12 Prostate cancer 56  7 All tissues (527) 363 177  *Pools of 5 unrelated normal breast tissues per sample (for a total of 30 unrelated individuals). Computational Analysis.

Microarray images were analyzed using GenePix Pro (Axon). Average values of the replicate spots of each miRNA were background-subtracted, normalized, and subjected to further analysis. Normalization was performed by using a per chip median normalization method, using the median array as a reference. Finally, miRNAs measured as present in at least the smallest of the two classes in a dataset were selected. Absent calls were thresholded to 4.5 prior to statistical analysis. This level is the average minimum intensity level detected in the experiments. MicroRNA nomenclature was according to the Genome Browser and the microRNA database at Sanger Center (Griffiths-Jones, S., Nucleic Acids Res 32: D109-11 (2004)); in case of discrepancies we followed the microRNA database. Differentially-expressed microRNA were identified by using the t test procedure within significance analysis of microarrays (SAM) (Tusher, V. G., et al., Proc Natl Acad Sci USA 98: 5116-21 (2001). SAM calculates a score for each gene on the basis of the change in expression relative to the standard deviation of all measurements. Within SAM, t test was used. The microRNA signatures were determined by applying nearest shrunken centroids method. This method identifies a subgroup of genes that best characterizes each solid cancer from its respective normal counterpart. The prediction error was calculated by means of 10-fold cross validation, and for each cancer, we obtained the miR signature that resulted in the minimal prediction error. A resampling test was performed by random permutation analysis to compute the p-value of the shared signature.

Example 1 Identification of a microRNA Expression Signature in Human Solid Cancers

Statistics

The combined cancers/normal tissue comparison was conducted using a reduced number of lung samples (80 cancer and 40 normal samples), in order to balance the different tissues numerically, yielding a total of 404 samples. For statistical analysis, 137 miRs, whose expression values were above 256 (threshold value) in at least 50% of the samples, were retained from the 228 that were measured. A T test was used to identify differentially-expressed microRNAs (Table 3). The p-values of the T test were corrected for multiple testing procedures and to control Type I error rates. Adjusted p-values were obtained by performing resampling with 500,000 permutations (Jung, S. H., et al. Biostatistics 6: 157-69 (2005)). This analysis was performed in order to evaluate the results by using the same method as Lu and co-workers (Lu, J., et al., Nature 435: 834-8 (2005)).

As an alternative to T test, significance analysis of microarrays (SAM) was used to identify differentially-expressed microRNAs. This procedure allows for the control of false detection rate (FDR). The delta was chosen to result in an FDR less than or equal to 0.01. microRNA subsets which result in the best tumor classification, i.e., which best predict the two classes (cancer and normal), were then identified using the method of the nearest shrunken centroids, as implemented in PAM (prediction analysis of microarray). The prediction error was calculated by means of 10-fold cross validation. The microRNAs were selected yielding the minimum misclassification error after cross-validation.

Results

By T-test, 43 differentially-expressed miRs with an adjusted p-value below 0.05 were obtained (Table 3). Twenty six miRs were overexpressed and 17 were under-expressed relative to corresponding normal tissues when the six solid cancers are grouped together (breast, colon, lung, pancreas, prostate, stomach). These results indicated that the spectrum of expressed miRNAs in solid cancers is very different from that of normal cells (43 out of 137 miRNAs, 31%). Using SAM, 49 miRNAs were identified as differentially-expressed, of which 34 were up-regulated (Table 4). Using PAM, 36 over-expressed miRNAs in cancer (indicated by positive cancer scores) and 21 down-regulated miRs (indicated by negative cancer scores) were identified as differentially-expressed (Table 5). However, these analyses are not tailored to identify alterations in miR expression that consistently result in transformation, because miR expression is heavily tissue-specific (He, L., et al. Nature 435: 828-833 (2005); also see FIG. 1 and FIG. 2).

The clustering of miRs based on expression profiles derived from 363 solid cancer and 177 normal samples using 228 miRs is shown in FIG. 1. The tree, which shows a very good separation between the different tissues, was constructed using 137 different miRNAs that were expressed in at least 50% of the samples used in the study.

TABLE 3 Differentially regulated miRs in 6 solid cancer types vs. normal tissues (T test stats.) *. Cancer Normal Test miR ID Mean Mean stat Raw p Adj p miR-21 #47 11.538663 9.648338 7.861136 2.00E−06 2.00E−06 miR-141 #137 9.024091 7.905398 6.238014 2.00E−06 2.00E−06 miR-212 #208 13.540651 14.33617 −6.57942 2.00E−06 2.00E−06 miR-128a prec #113 12.32588 13.522675 −6.76388 2.00E−06 2.00E−06 miR-138-2 #133 11.739557 13.144746 −7.01204 2.00E−06 2.00E−06 miR-218-2 #221 11.279787 12.539366 −7.40557 2.00E−06 2.00E−06 miR-23b #51 14.169748 15.949736 −8.37744 2.00E−06 2.00E−06 miR-195 #184 10.343991 9.172985 5.763262 2.00E−06 1.00E−05 miR-212 prec #209 12.686966 13.661763 −5.83132 4.00E−06 1.00E−05 miR-29b-2 #95 11.27556 9.940731 5.660854 2.00E−06 1.40E−05 miR-199a-1 #191 10.032008 8.920183 5.528849 2.00E−06 3.00E−05 miR-9-3 #28 11.461922 12.570412 −5.43006 2.00E−06 4.60E−05 miR-128a #114 13.024235 13.856624 −5.35102 6.00E−06 7.20E−05 let-7a-1 #1 12.616569 13.455246 −5.35346 2.00E−06 7.20E−05 let-7b #5 13.42636 14.068521 −5.17701 1.00E−05 0.000146 miR-16-2 #39 10.460707 9.305895 5.048375 4.00E−06 0.000224 miR-199a-2 #192 9.714225 8.759237 4.862553 1.00E−05 0.000494 miR-152 prec #151 11.388676 12.357529 −4.83716 2.00E−06 0.00053 miR-16-1 #38 10.443169 9.338182 4.755258 1.00E−05 0.00071 miR-30d #72 13.982017 14.775206 −4.5707 1.20E−05 0.001476 miR-34a #78 10.675566 9.63769 4.467301 2.60E−05 0.00217 miR-17-5p #41 11.567244 10.281468 4.341834 3.80E−05 0.0034 miR-128b #115 10.930395 9.947746 4.304764 3.80E−05 0.003912 miR-20a #46 11.409852 10.19284 4.304678 3.20E−05 0.003912 miR-181b-1 prec #211 9.577504 8.804294 4.285968 4.80E−05 0.004126 miR-132 #121 9.599947 8.775966 4.284737 5.60E−05 0.004126 miR-200b #195 9.475221 8.527243 4.221511 4.00E−05 0.0052 let-7a-3 #4 10.436089 9.511546 4.08952 0.000104 0.008242 miR-138-1 #132 8.299613 9.200253 −4.05204 5.60E−05 0.00931 miR-29c #65 11.291005 10.326912 4.019385 0.000144 0.010312 miR-29a #62 11.381359 10.461075 4.013697 0.00015 0.010398 miR-96 #86 11.37218 12.136636 −3.94825 0.000138 0.012962 miR-191 #177 13.498207 12.729872 3.817228 0.000158 0.02015 miR-27a #59 10.399338 9.548582 3.715048 0.000344 0.028096 let-7g #15 10.819688 10.01157 3.653239 0.000426 0.033874 miR-9-1 #24 10.102819 9.212988 3.651886 0.000388 0.033874 miR-125a #107 10.960998 10.005312 3.651356 0.000452 0.033874 miR-95 #84 9.435733 8.751331 3.59406 0.000478 0.039594 miR-155 #157 12.505359 13.231221 −3.58369 0.000614 0.040394 miR-199b #194 9.755066 9.082751 3.55934 0.000588 0.04314 miR-24-2 #54 12.611696 11.612557 3.518774 0.00087 0.048278 let-7e #11 12.497795 13.055093 −3.51589 0.00054 0.048354 miR-92-1 #81 16.081074 16.592426 −3.50446 0.000928 0.049828 * Forty-three miRs have an adjusted p-value lower than 0.05. Twenty-six miRs are overexpressed and 17 down-regulated in breast, colon, lung, pancreas, prostate, stomach carcinomas.

TABLE 4 Differentially regulated miRs in 6 solid cancer types vs. normal tissues (SAM, significance analysis of microarrays) *. d. p. q. R. miR ID value stdev value value fold miR-21 #47 3.156 0.24 0 0 2.593 miR-23b #51 −3.117 0.212 0 0 0.443 miR-138-2 #133 −2.514 0.2 0 0 0.402 miR-218-2 #221 −2.383 0.17 0 0 0.384 miR-29b-2 #95 2.246 0.236 0 0 1.868 miR-128a prec #113 −2.235 0.177 0 0 0.368 miR-195 #184 2.085 0.203 0 0 1.695 miR-141 #137 2.08 0.179 0 0 2.459 miR-199a-1 #191 1.987 0.201 0 0 1.945 miR-9-3 #28 −1.97 0.204 0 0 0.433 miR-16-2 #39 1.966 0.229 0 0 1.788 miR-17-5p #41 1.964 0.296 0 0 0.725 miR-20a #46 1.898 0.283 0 0 0.969 miR-16-1 #38 1.87 0.232 0 0 1.447 miR-212 prec #209 −1.854 0.167 0 0 0.509 miR-34a #78 1.756 0.232 0 0 1.219 miR-152 prec #151 −1.734 0.2 0 0 0.46 miR-199a-2 #192 1.721 0.196 0 0 1.838 miR-128b #115 1.674 0.228 0 0 1.266 miR-212 #208 −1.659 0.121 0 0 0.627 let-7a-1 #1 −1.628 0.157 0 0 0.461 miR-200b #195 1.626 0.225 0 0 1.432 miR-128a #114 −1.619 0.156 0 0 0.511 miR-29c #65 1.611 0.24 0 0 1.225 let-7a-3 #4 1.581 0.226 0 0 1.109 miR-29a #62 1.565 0.229 0 0 1.706 miR-24-2 #54 1.555 0.284 0 0 0.831 miR-138-1 #132 −1.551 0.222 0 0 0.432 miR-125a #107 1.541 0.262 0 0 1.164 miR-106a #99 1.514 0.275 0 0 0.952 miR-132 #121 1.496 0.192 0 0 2.158 miR-30d #72 −1.491 0.174 0 0 0.424 miR-9-1 #24 1.478 0.244 0 0 0.763 miR-27a #59 1.448 0.229 0 0 1.174 miR-181b-1 prec #211 1.435 0.18 0 0 1.525 let-7g #15 1.394 0.221 0 0 1.072 miR-96 #86 −1.384 0.194 0 0 0.519 miR-191 #177 1.372 0.201 0 0 1.165 miR-93-1 #83 1.363 0.266 0 0 0.775 miR-136 #130 −1.355 0.267 0 0 0.364 miR-205 #201 1.343 0.309 0 0 1.281 miR-185 #170 1.287 0.222 0.001 0.001 0.609 miR-125b-1 #109 1.262 0.283 0.001 0.001 1.215 miR-10a #30 1.252 0.227 0.001 0.001 1.643 miR-95 #84 1.247 0.19 0.001 0.001 1.509 miR-199b #194 1.228 0.189 0.001 0.001 1.246 miR-10b #32 1.219 0.232 0.002 0.001 1.342 let-7i #10 1.216 0.203 0.002 0.001 1.026 miR-210 #205 1.213 0.237 0.002 0.001 1.088 * Thirty five miRs are over-expressed and 14 are down-regulated in breast, colon, lung, pancreas, prostate, stomach carcinomas (Delta = 0.9, FDR = 0.001).

TABLE 5 MicroRNAs selected by PAM (prediction analysis of microarray) in 6 solid cancer types vs. normal tissues miR ID Solid cancer score Normal tissues score miR-21 #47 0.0801 −0.2643 miR-138-2 #133 −0.055 0.1815 miR-218-2 #221 −0.0535 0.1765 miR-23b #51 −0.0516 0.17 miR-128a prec #113 −0.0498 0.1642 miR-29b-2 #95 0.0457 −0.1508 miR-195 #184 0.0404 −0.1333 miR-17-5p #41 0.0383 −0.1263 miR-9-3 #28 −0.0357 0.1176 miR-212 prec #209 −0.0342 0.1129 miR-20a #46 0.0322 −0.1061 miR-141 #137 0.0322 −0.1061 miR-199a-1 #191 0.0319 −0.1053 miR-16-2 #39 0.0315 −0.1037 miR-152 prec #151 −0.0283 0.0933 miR-16-1 #38 0.0277 −0.0913 miR-34a #78 0.0269 −0.0886 miR-212 #208 −0.0265 0.0875 let-7a-1 #1 −0.0264 0.0872 miR-128a #114 −0.0259 0.0855 miR-128b #115 0.0254 −0.0839 miR-24-2 #54 0.0244 −0.0803 miR-29c #65 0.0224 −0.0738 miR-199a-2 #192 0.0223 −0.0736 let-7a-3 #4 0.0221 −0.073 miR-191 #177 0.0188 −0.062 miR-125a #107 0.0186 −0.0613 miR-30d #72 −0.0185 0.061 miR-29a #62 0.0184 −0.0608 miR-106a #99 0.0177 −0.0584 miR-93-1 #83 0.0163 −0.0537 miR-200b #195 0.0159 −0.0524 let-7g #15 0.0158 −0.0521 miR-27a #59 0.0157 −0.0518 miR-96 #86 −0.0156 0.0514 let-7b #5 −0.0152 0.0501 miR-138-1 #132 −0.0151 0.0499 miR-9-1 #24 0.0136 −0.0448 miR-181b-1 prec #211 0.0134 −0.0442 miR-155 #157 −0.0128 0.0423 miR-132 #121 0.0127 −0.0418 miR-136 #130 −0.0112 0.037 let-7i #10 0.0103 −0.034 miR-210 #205 0.0074 −0.0245 miR-205 #201 0.0073 −0.024 *miR-185 #170 0.0071 −0.0234 miR-24-1 #52 0.007 −0.023 miR-199b #194 0.0064 −0.021 miR-125b-1 #109 0.006 −0.0199 miR-206 prec #203 −0.005 0.0166 miR-10a #30 0.0045 −0.015 miR-95 #84 0.0045 −0.0149 let-7c #11 −0.0039 0.013 miR-124a-3 #106 −0.0028 0.0091 miR-10b #32 0.002 −0.0066 miR-185 prec #171 −0.0014 0.0047 miR-92-1 #81 −2.00E−04 5.00E−04 *T = 1.5 and misclassification error = 0.176. Thirty six over-expressed miRs in cancer are indicated by positive cancer scores; 21 down-regulated miRs are indicated by negative cancer scores.

Example 2 Identification of microRNA Expression Signatures Associated with Various Human Solid Cancers

Results

To identify microRNAs that are prognostic for cancer status associated with solid tumors, without incurring bias due to tissue specificity, an alternative approach was used. First, six tissue-specific signatures, one for each cancer histotype, were obtained by performing independent PAM tests (summarized in Tables 6 and 7) Specific signatures for each cancer are shown in Tables 8-13: e.g., breast-Table 8; colon-Table 9; lung-Table 10; pancreas-Table 11; prostate-Table 12; stomach-Table 13. Using these data, deregulated microRNAs that were shared among the different histotype miRNA signatures were identified (Table 14). In order to compute the p-values for this comparative analysis, a re-sampling test with 1,000,000 random permutations on the miRNA identity was performed. The p-value was defined as the relative frequency of simulation scores exceeding the real score. Twenty-one misregulated microRNAs that were common to at least 3 types of solid cancers (p-value=2.5×10⁻³) were identified (Table 14).

TABLE 6 MicroRNAs used to classify human cancers and normal tissues*. Up- Down- Misclassification regulated regulated error after 10 fold Cancer miRs miRs cross validation Breast 15 12 0.08 Colon 21 1 0.09 Lung 35 3 0.31 Pancreas 55 2 0.02 Prostate 39 6 0.11 Stomach 22 6 0.19 *Median normalization was performed and the method of the nearest shrunken centroids was used to select predictive miRNAs.

TABLE 7 Deregulated microRNAs in solid common cancers*. PAM Up- SAM Up- PAM Down- SAM Down- Cancer regulated regulated regulated regulated Breast 15  3 (FDR = 0.33) 12 47 Colon 21 42 (FDR <= 0.06) 1 5 Lung 35 38 (FDR <= 0.01) 3 3 Pancreas 55 50 (FDR <= 0.01) 2 8 Stomach 22 22 (FDR = 0.06) 6 4 Prostate 39 49 (FDR = 0.06) 6 3 *Prediction analysis of microarrays (PAM) identifies those genes which best characterize cancers and normal tissues, whilst significance analysis of microarrays (SAM) identifies all those which have differential expression in the two classes. False detection rates (FDR) computed in SAM are indicated in parenthesis.

TABLE 8 MicroRNAs selected by prediction analysis of microarray (PAM) in breast cancer (cancer vs. normal tissues) *. miR Cancer score Normal score miR-21 (#47) 0.0331 −0.4364 miR-29b-2 (#95) 0.0263 −0.3467 miR-146 (#144) 0.0182 −0.2391 miR-125b-2 (#111) −0.0174 0.2286 miR-125b-1 (#109) −0.0169 0.222 miR-10b (#32) −0.0164 0.2166 miR-145 (#143) −0.0158 0.2076 miR-181a (#158) 0.0153 −0.201 miR-140 (#136) −0.0122 0.1613 miR-213 (#160) 0.0116 −0.1527 miR-29a prec (#63) 0.0109 −0.1441 miR-181b-1 (#210) 0.0098 −0.1284 miR-199b (#194) 0.0089 −0.1172 miR-29b-1 (#64) 0.0084 −0.1111 miR-130a (#120) −0.0076 0.1001 miR-155 (#157) 0.0072 −0.0951 let-7a-2 (#3) −0.0042 0.0554 miR-205 (#201) −0.004 0.0533 miR-29c (#65) 0.0032 −0.0423 miR-224 (#228) −0.003 0.0399 miR-100 (#91) −0.0021 0.0283 miR-31 (#73) 0.0017 −0.022 miR-30c (#70) −7.00E−04   0.009 miR-17-5p (#41) 7.00E−04 −0.0089 miR-210 (#205) 4.00E−04 −0.0057 miR-122a (#101) 4.00E−04 −0.005 miR-16-2 (#39) −1.00E−04   0.0013 * 27 miRs selected, misclassification error after cross validation of 0.008. Seventeen overexpressed miRs in cancer are indicated by positive cancer scores; 12 down-regulated miRs are indicated by negative cancer scores.

TABLE 9 MicroRNAs selected by prediction analysis of microarray (PAM) in colon (cancer vs. normal tissues)*. miR Cancer score Normal score miR-24-1 (#52) 0.0972 −0.5589 miR-29b-2 (#95) 0.0669 −0.3845 miR-20a (#46) 0.0596 −0.3424 miR-10a (#30) 0.0511 −0.2938 miR-32 (#75) 0.0401 −0.2306 miR-203 (#197) 0.0391 −0.2251 miR-106a (#99) 0.0364 −0.2094 miR-17-5p (#41) 0.0349 −0.2005 miR-30c (#70) 0.0328 −0.1888 miR-223 (#227) 0.0302 −0.1736 miR-126* (#102) 0.0199 −0.1144 miR-128b (#115) 0.0177 −0.102 miR-21 (#47) 0.0162 −0.0929 miR-24-2 (#54) 0.0145 −0.0835 miR-99b prec (#88) 0.0125 −0.0721 miR-155 (#157) 0.0092 −0.0528 miR-213 (#160) 0.0091 −0.0522 miR-150 (#148) 0.0042 −0.0243 miR-107 (#100) 0.003 −0.0173 miR-191 (#177) 0.0028 −0.0159 miR-221 (#224) 0.002 −0.0116 miR-9-3 (#28) −0.0014 0.0083 *22 miRs selected, misclassification error after cross validation of 0.09. Twenty-one over-expressed miRs in cancer are indicated by positive cancer scores; 1 down-regulated miR is indicated by a negative cancer score.

TABLE 10 MicroRNAs selected by prediction analysis of microarray (PAM) in lung cancer (cancer vs. normal tissues)*. miR Cancer score Normal score miR-21 (#47) 0.175 −0.175 miR-205 (#201) 0.1317 −0.1317 miR-200b (#195) 0.1127 −0.1127 miR-9-1 (#24) 0.1014 −0.1014 miR-210 (#205) 0.0994 −0.0994 miR-148 (#146) 0.0737 −0.0737 miR-141 (#137) 0.0631 −0.0631 miR-132 (#121) 0.0586 −0.0586 miR-215 (#213) 0.0575 −0.0575 miR-128b (#115) 0.0559 −0.0559 let-7g (#15) 0.0557 −0.0557 miR-16-2 (#39) 0.0547 −0.0547 miR-129-1/2 prec (#118) 0.0515 −0.0515 miR-126* (#102) −0.0406 0.0406 miR-142-as (#139) 0.0366 −0.0366 miR-30d (#72) −0.0313 0.0313 miR-30a-5p (#66) −0.0297 0.0297 miR-7-2 (#21) 0.0273 −0.0273 miR-199a-1 (#191) 0.0256 −0.0256 miR-127 (#112) 0.0254 −0.0254 miR-34a prec (#79) 0.0214 −0.0214 miR-34a (#78) 0.0188 −0.0188 miR-136 (#130) 0.0174 −0.0174 miR-202 (#196) 0.0165 −0.0165 miR-196-2 (#188) 0.0134 −0.0134 miR-199a-2 (#192) 0.0126 −0.0126 let-7a-2 (#3) 0.0109 −0.0109 miR-124a-1 (#104) 0.0081 −0.0081 miR-149 (#147) 0.0079 −0.0079 miR-17-5p (#41) 0.0061 −0.0061 miR-196-1 prec (#186) 0.0053 −0.0053 miR-10a (#30) 0.0049 −0.0049 miR-99b prec (#88) 0.0045 −0.0045 miR-196-1 (#185) 0.0044 −0.0044 miR-199b (#194) 0.0039 −0.0039 miR-191 (#177) 0.0032 −0.0032 miR-195 (#184) 7.00E−04 −7.00E−04 miR-155 (#157) 7.00E−04 −7.00E−04 *38 miRs selected, misclassification error after cross validation of 0.31. Thirty-five over-expressed miRs in cancer are indicated by positive cancer scores; 3 down-regulated miRs are indicated by negative cancer scores.

TABLE 11 MicroRNAs selected by prediction analysis of microarray (PAM) in pancreatic cancer (cancer vs. normal tissues)*. miR Cancer score Normal score miR-103-2 (#96) 0.4746 −1.582 miR-103-1 (#97) 0.4089 −1.3631 miR-24-2 (#54) 0.4059 −1.3529 miR-107 (#100) 0.3701 −1.2336 miR-100 (#91) 0.3546 −1.182 miR-125b-2 (#111) 0.3147 −1.0489 miR-125b-1 (#109) 0.3071 −1.0237 miR-24-1 (#52) 0.2846 −0.9488 miR-191 (#177) 0.2661 −0.887 miR-23a (#50) 0.2586 −0.8619 miR-26a-1 (#56) 0.2081 −0.6937 miR-125a (#107) 0.1932 −0.644 miR-130a (#120) 0.1891 −0.6303 miR-26b (#58) 0.1861 −0.6203 miR-145 (#143) 0.1847 −0.6158 miR-221 (#224) 0.177 −0.59 miR-126* (#102) 0.1732 −0.5772 miR-16-2 (#39) 0.1698 −0.5659 miR-146 (#144) 0.1656 −0.552 miR-214 (#212) 0.1642 −0.5472 miR-99b (#89) 0.1636 −0.5454 miR-128b (#115) 0.1536 −0.512 miR-155 (#157) −0.1529 0.5098 miR-29b-2 (#95) 0.1487 −0.4956 miR-29a (#62) 0.1454 −0.4848 miR-25 (#55) 0.1432 −0.4775 miR-16-1 (#38) 0.1424 −0.4746 miR-99a (#90) 0.1374 −0.4581 miR-224 (#228) 0.1365 −0.4549 miR-30d (#72) 0.1301 −0.4336 miR-92-2 (#82) 0.116 −0.3865 miR-199a-1 (#191) 0.1158 −0.3861 miR-223 (#227) 0.1141 −0.3803 miR-29c (#65) 0.113 −0.3768 miR-30b (#68) 0.1008 −0.3361 miR-129-1/2 (#117) 0.1001 −0.3337 miR-197 (#189) 0.0975 −0.325 miR-17-5p (#41) 0.0955 −0.3185 miR-30c (#70) 0.0948 −0.316 miR-7-1 (#19) 0.0933 −0.311 miR-93-1 (#83) 0.0918 −0.3061 miR-140 (#136) 0.0904 −0.3015 miR-30a-5p (#66) 0.077 −0.2568 miR-132 (#121) 0.0654 −0.2179 miR-181b-1 (#210) 0.0576 −0.1918 miR-152 prec (#151) −0.0477 0.1591 miR-23b (#51) 0.0469 −0.1562 miR-20a (#46) 0.0452 −0.1507 miR-222 (#225) 0.0416 −0.1385 miR-27a (#59) 0.0405 −0.1351 miR-92-1 (#81) 0.0332 −0.1106 miR-21 (#47) 0.0288 −0.0959 miR-129-1/2 prec (#118) 0.0282 −0.0939 miR-150 (#148) 0.0173 −0.0578 miR-32 (#75) 0.0167 −0.0558 miR-106a (#99) 0.0142 −0.0473 miR-29b-1 (#64) 0.0084 −0.028 *57 miRs selected, misclassification error after cross validation of 0.02. Fifty-seven miRs are over-expressed and 2 are down-regulated in cancer (indicated by positive and negative scores, respectively).

TABLE 12 MicroRNAs selected by prediction analysis of microarray (PAM) in prostate cancer (cancer vs. normal tissues) *. miR Cancer score Normal score let-7d (#8) 0.0528 −0.4227 miR-128a prec (#113) −0.0412 0.3298 miR-195 (#184) 0.04 −0.3199 miR-203 (#197) 0.0356 −0.2851 let-7a-2 prec (#2) −0.0313 0.2504 miR-34a (#78) 0.0303 −0.2428 miR-20a (#46) 0.029 −0.2319 miR-218-2 (#221) −0.0252 0.2018 miR-29a (#62) 0.0247 −0.1978 miR-25 (#55) 0.0233 −0.1861 miR-95 (#84) 0.0233 −0.1861 miR-197 (#189) 0.0198 −0.1587 miR-135-2 (#128) 0.0198 −0.1582 miR-187 (#173) 0.0192 −0.1535 miR-196-1 (#185) 0.0176 −0.1411 miR-148 (#146) 0.0175 −0.1401 miR-191 (#177) 0.017 −0.136 miR-21 (#47) 0.0169 −0.1351 let-7i (#10) 0.0163 −0.1303 miR-198 (#190) 0.0145 −0.1161 miR-199a-2 (#192) 0.0136 −0.1088 miR-30c (#70) 0.0133 −0.1062 miR-17-5p (#41) 0.0132 −0.1053 miR-92-2 (#82) 0.012 −0.0961 miR-146 (#144) 0.0113 −0.0908 miR-181b-1 prec (#211) 0.011 −0.0878 miR-32 (#75) 0.0109 −0.0873 miR-206 (#202) 0.0104 −0.083 miR-184 prec (#169) 0.0096 −0.0764 miR-29a prec (#63) −0.0095 0.076 miR-29b-2 (#95) 0.0092 −0.0739 miR-149 (#147) −0.0084 0.0676 miR-181b-1 (#210) 0.0049 −0.0392 miR-196-1 prec (#186) 0.0042 −0.0335 miR-93-1 (#83) 0.0039 −0.0312 miR-223 (#227) 0.0038 −0.0308 miR-16-1 (#38) 0.0028 −0.0226 miR-101-1 prec (#92) 0.0015 −0.0123 miR-124a-1 (#104) 0.0015 −0.0119 miR-26a-1 (#56) 0.0015 −0.0119 miR-214 (#212) 0.0013 −0.0105 miR-27a (#59) 0.0011 −0.0091 miR-24-1 (#53) −8.00E−04   0.0067 miR-106a (#99) 7.00E−04 −0.0057 miR-199a-1 (#191) 4.00E−04 −0.0029 * T = 1, 45 miRs selected, misclassification error after cross validation of 0.11. Thirty-nine over-expressed miRs in cancer are indicated by positive cancer scores; 6 downregulated miRs are indicated by negative cancer scores.

TABLE 13 MicroRNAs selected by prediction analysis of microarray (PAM) in stomach cancer (cancer vs. normal tissues) *. miR Cancer score Normal score miR-223 (#227) 0.1896 −0.1806 miR-21 (#47) 0.1872 −0.1783 miR-218-2 (#221) −0.1552 0.1478 miR-103-2 (#96) 0.1206 −0.1148 miR-92-2 (#82) 0.1142 −0.1088 miR-25 (#55) 0.1097 −0.1045 miR-136 (#130) −0.1097 0.1045 miR-191 (#177) 0.0946 −0.0901 miR-221 (#224) 0.0919 −0.0876 miR-125b-2 (#111) 0.0913 −0.0869 miR-103-1 (#97) 0.0837 −0.0797 miR-214 (#212) 0.0749 −0.0713 miR-222 (#225) 0.0749 −0.0713 miR-212 prec (#209) −0.054 0.0514 miR-125b-1 (#109) 0.0528 −0.0503 miR-100 (#91) 0.0526 −0.0501 miR-107 (#100) 0.0388 −0.0369 miR-92-1 (#81) 0.0369 −0.0351 miR-96 (#86) −0.0306 0.0291 miR-192 (#178) 0.0236 −0.0224 miR-23a (#50) 0.022 −0.021 miR-215 (#213) 0.0204 −0.0194 miR-7-2 (#21) 0.0189 −0.018 miR-138-2 (#133) −0.0185 0.0176 miR-24-1 (#52) 0.0151 −0.0144 miR-99b (#89) 0.0098 −0.0093 miR-33b (#76) −0.0049 0.0046 miR-24-2 (#54) 0.0041 −0.0039 * T = 1, 28 miRs selected, misclassification error after cross validation of 0.19. Twenty-two over-expressed miRs in cancer are indicated by positive cancer scores; 6 down-regulated miRs are indicated by negative cancer scores.

TABLE 14 The microRNAs shared by the signatures of the 6 solid cancers*. miR N Tumor Type miR-21 6 Breast Colon Lung Pancreas Prostate Stomach miR-17-5p 5 Breast Colon Lung Pancreas Prostate miR-191 5 Colon Lung Pancreas Prostate Stomach miR-29b-2 4 Breast Colon Pancreas Prostate miR-223 4 Colon Pancreas Prostate Stomach miR-128b 3 Colon Lung Pancreas miR-199a-1 3 Lung Pancreas Prostate miR-24-1 3 Colon Pancreas Stomach miR-24-2 3 Colon Pancreas Stomach miR-146 3 Breast Pancreas Prostate miR-155 3 Breast Colon Lung miR-181b-1 3 Breast Pancreas Prostate miR-20a 3 Colon Pancreas Prostate miR-107 3 Colon Pancreas Stomach miR-32 3 Colon Pancreas Prostate miR-92-2 3 Pancreas Prostate Stomach miR-214 3 Pancreas Prostate Stomach miR-30c 3 Colon Pancreas Prostate miR-25 3 Pancreas Prostate Stomach miR-221 3 Colon Pancreas Stomach miR-106a 3 Colon Pancreas Prostate *The list includes 21 commonly up-regulated microRNAs in 3 or more (N) types of solid cancers (p-value = 2.5 × 10⁻³).

To maximize concision, the mean absolute expression levels of the deregulated miRs for the 6 cancer/normal pairs were computed. Using the expression level of miRs in the comprehensive subset, the different tissues were correctly classified, irrespective of the disease status (FIG. 3).

FIG. 4 shows differential expression of the common microRNAs across the different tumor tissues, in relation to the normal tissues. The tree displays the different cancer types according to fold changes in the miRNA subset. Prostate, colon, stomach and pancreatic tissues are most similar among them, while lung and breast tissues were represented by a fairly different signature (FIG. 4). This tree clearly shows which miRNAs are associated with a particular cancer histotype.

Strikingly, miR-21, miR-191 and miR-17-5p are significantly over-expressed in all, or in 5 out of 6, of the tumor types that were considered. miR-21 was reported to be over-expressed in glioblastoma and to have anti-apoptotic properties (Chan, J. A., et al., Cancer Res. 65: 6029-6033 (2005)). Lung cancer shares a portion of its signature with breast cancer and a portion with the other solid tumors, including miR-17/20/92, all three of which are members of the microRNA cluster that actively cooperates with c-Myc to accelerate lymphomagenesis (He, L., et al., Nature 435: 828-833 (2005)). The identification of these microRNAs as being over-expressed is an excellent confirmation of our approach. A second miRNA group that is activated includes miR-210 and miR-213, together with miR-155, which was already reported to be amplified in large cell lymphomas (Eis, P. S., et al., Proc. Natl. Acad. Sci. USA 102: 3627-3632 (2005)), children with Burkitt lymphoma (Metzler, M., et al., Genes Chromosomes Cancer 39:167-169 (2004)) and various B cell lymphomas (Kluiver, J, et al., J. Pathol., e-published online, Jul. 22, 2005). These microRNAs are the only ones up-regulated in breast and lung cancer. miR-218-2 is consistently down-regulated in colon, stomach, prostate and pancreas cancers, but not in lung and breast carcinomas.

Several observations strengthen these results. First, in this study, the expression levels of both the precursor pre-miRNA and the mature miRNA were determined for the majority of genes. Of note, with the exception of miR-212 and miR-128a, in all other instances, the abnormally-expressed region was that corresponding to the active gene product. Second, as shown in FIG. 3, the expression variation of the miRNAs in the comprehensive subset was often univocal (namely, down- or up-regulation) across the different types of cancers, suggesting a common mechanism in human tumorigenesis. Third, the microarray data were validated by solution hybridization for 12 breast samples (miR-125b, miR-145 and miR-21; Iorio, M. V., et al., Cancer Res. 65: 7065-7070 (2005)) and 17 endocrine pancreatic and normal samples (miR-103, miR-155 and miR-204; data not shown), strongly confirming the accuracy of the microarray data.

Example 3 Identification of Predicted Targets for microRNAs that are Deregulated in Solid Tumors

Materials and Methods:

Tumor Suppressor and Oncogene Target Predictions

The most recent TargetScan predictions (April 2005) were used to identify putative microRNA targets. These include essentially the 3′UTR targets reported by Lewis et al. (Lewis, B. P., et al, Cell 120: 15-20 (2005)), with a few changes arising from updated gene boundary definitions from the April 2005 UCSC Genome Browser mapping of RefSeq mRNAs to the hgl7 human genome assembly. Among the putative targets, known cancer genes (tumor suppressors and oncogenes) were specified according to their identification in the Cancer Gene Census or as reported by OMIM.

Target In Vitro Assays

For luciferase reporter experiments, 3′ UTR segments of Rb1, TGFBR2 and Plag1 that are predicted to interact with specific cancer-associated microRNAs were amplified by PCR from human genomic DNA and inserted into the pGL3 control vector (Promega) using the XbaI site immediately downstream from the stop codon of luciferase. The human megakaryocytic cell line, MEG-01, was grown in 10% FBS in RPMI medium 1640, supplemented with 1× nonessential amino acid and 1 mmol sodium pyruvate at 37° C. in a humidified atmosphere of 5% CO₂. The cells were co-transfected in 12-well plates by using siPORT neoFX (Ambion, Austin, Tex.), according to the manufacturer's protocol, with 0.4 μg of the firefly luciferase reporter vector and 0.08 μg of the control vector containing Renilla luciferase, pRL-TK (Promega). For each well, microRNA oligonucleotides (Dharmacon Research, Lafayette, Colo.) and anti-sense or scrambled oligonucleotides (Ambion) were used at a concentration of 10 nM. Firefly and Renilla luciferase activities were measured consecutively at 24 h post transfection using dual-luciferase assays (Promega).

Western Blotting for RB1

Levels of RB1 protein were quantified using a mouse monoclonal anti-RB1 antibody (Santa Cruz, Calif.) using standard procedures for Western blotting. The normalization was performed with mouse monoclonal anti-Actin antibody (Sigma).

Results

The functional significance of microRNA deregulation in cancer needs to be understood. In solid tumors, it appears that the most common microRNA event is gain of expression, while loss of expression in cancer is a more limited event, and more tissue specific. We used a three-step consequential approach in the following order: first, “in silico” prediction of targets, then luciferase assay for first validation of cancer relevant targets and finally, ex vivo tumor correlation between miRNA expression (by microarray) and target protein expression (by Western blotting) for a specific miRNA:mRNA interactor pair. Relevant targets for cancer miRNAs could be either recessive (e.g., tumor suppressors) or dominant (e.g., oncogenes) cancer genes. To test the hypothesis that microRNAs that are deregulated in solid tumors target known oncogenes or tumor suppressors, the predicted targets for these miRNAs were determined using TargetScan, a database of conserved 3′ UTR microRNA targets (Lewis, B. P., et al, Cell 120: 15-20 (2005)). TargetScan contained 5,121 predictions for 18 miRNAs that are dysregulated in solid tumors, in the total 22,402 (26.5%) predictions. One hundred fifteen out of 263 (44%) well-known cancer genes were predicted as targets for these 18 miRNAs (Table 15). Because a high percentage of cancer genes are targeted by miRs that are deregulated in solid tumors, it is unlikely that these predictions are due to chance (P<0.0001 at Fisher exact-test).

In silico predictions for three different cancer genes, Retinoblastoma (Rb), TGF-beta-2 receptor (TGFBR2), and pleiomorphic adenoma gene 1 (PLAG1), were confirmed experimentally by in vitro assays. Using a luciferase reporter assay, three microRNAs tested (miR-106a, miR-20a and miR-26a-1) caused a significant reduction of protein translation relative to the scrambled control oligoRNAs in transfected MEG-01 cells (FIG. 6). Retinoblastoma 3′UTR, for example, was found to interact functionally with miR-106a. The biological significance of this miRNA:mRNA interaction is reinforced by previous reports showing that the Rb1 gene is normally transcribed in colon cancers, whilst various fractions of cells do not express Rb1 protein (Ali, A. A., et al., FASEB J. 7:931-937 (1993)). This finding suggests the existence of a post-transcriptional mechanism for regulating Rb1 that could be explained by concomitant miR-106a over-expression in colon carcinoma (FIG. 4). Furthermore, mir-20a is down-regulated in breast cancer (FIG. 4) and TFGBR2 protein is expressed in the epithelium of breast cancer cells (Buck, M. B., et al., Clin. Cancer Res. 10:491-498 (2004)). Conversely, the over-expression of mir-20a in colon cancer may represent a novel mechanism for down-regulating TGFBR2, in addition to mutational inactivation (Biswas, S., et al., Cancer Res. 64:687-692 (2004)).

Finally, a set of patient samples was tested to verify whether RB1 protein expression correlates with miR-106a expression (FIG. 5 and FIG. 6B). As expected, in gastric, prostate and lung tumor samples RB1 was down-regulated (in respect to the paired normal) and miR-106a was found to be over-expressed, while in breast tumor samples, where miR-106a is slightly down-regulated (FIG. 5 and FIG. 6B), RB1 is expressed at slightly higher levels then in the paired normal control.

These experimental proofs reinforce the hypothesis that key cancer genes are regulated by aberrant expression of miRs in solid cancers. These data add novel examples to the list of microRNA with important cancer gene targets, as previously shown by Johnsson et al. (Johnson, S. M., et al., Cell 120: 635-647 (2005)) for the let-7:Ras interaction, O'Donnell et al. (O'Donnell, K. A., et al., Nature 435:839-843 (2005)) for the miR-17-5p:cMyc interaction, and Cimmino et al. (Cimmino, A., et al., Proc. Natl. Acad. Sci. USA 102:13944-13949 (2005)) for the mir-16:Bcl2 interaction. Notably, miR-17-5p and miR-16 are members of the miRNA solid cancer signature described herein.

TABLE 15 Oncogenes and tumor suppressor genes predicted by TargetScanS as targets or microRNAs from the comprehensive cancer subset.* miRNA gene Gene Name Gene description miR-26a, miR-146 ABL2 v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene) miR-107 AF5q31 ALL1 fused gene from 5q31 miR-20, miR-125b AKT3 v-akt murine thymoma viral oncogene homolog 3 miR-26a, miR-155 APC adenomatosis polyposis coli miR-125b miR-26a, miR-218 ARHGEF12 RHO guanine nucleotide exchange factor (GEF) 12 (LARG) miR-107, miR-221 ARNT aryl hydrocarbon receptor nuclear translocator miR-192 ATF1 activating transcription factor 1 miR-26a ATM Ataxia telangiectasia mutated (includes complementation groups A, C and D) miR-24 AXL AXL receptor tyrosine kinase miR-26a, miR-107, BCL11A B-cell CLL/lymphoma 11A miR-146, miR-155 miR-138, miR-92 miR-20 BCL11B B-cell CLL/lymphoma 11B (CTIP2) miR-21 BCL2 B-cell CLL/lymphoma 2 miR-26a, miR-26a BCL6 B-cell CLL/lymphoma 6 (zinc finger protein 51) miR-20, miR-92 BCL9 B-cell CLL/lymphoma 9 miR-26a, miR-223 CBFB core-binding factor, beta subunit miR-221, miR-125b miR-218 CCDC6 coiled-coil domain containing 6 miR-20 CCND1 cyclin D1 (PRAD1: parathyroid adenomatosis 1) miR-26a, miR-20 CCND2 cyclin D2 miR-26a, miR-107, CDK6 cyclin-dependent kinase 6 miR-92 miR-20 CDKN1A cyclin-dependent kinase inhibitor 1A (p21, Cip1) miR-221, miR-92 CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2) miR-24 CDX2 caudal type homeo box transcription factor 2 miR-92 CEBPA CCAAT/enhancer binding protein (C/EBP), alpha miR-26a CLTC clathrin, heavy polypeptide (Hc) miR-218 COL1A1 collagen, type I, alpha 1 miR-26a CREBBP CREB binding protein (CBP) miR-20 CRK v-crk avian sarcoma virus CT10 oncogene homolog miR-20 CSF1 colony stimulating factor 1 (macrophage) miR-221, miR-192 DDX6 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54 kD) miR-138 DEK DEK oncogene (DNA binding) miR-20 E2F1 E2F transcription factor 1 miR-20 ELK3 ELK3, ETS-domain protein (SRF accessory protein 2) miR-24 ELL ELL gene (11-19 lysine-rich leukemia gene) miR-26a, miR-138 ERBB4 v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4 miR-221, miR-155, ETS1 v-ets avian erythroblastosis virus E26 oncogene miR-125b homolog 1 miR-20 ETV1 ets variant gene 1 miR-125b ETV6 ets variant gene 6 (TEL oncogene) miR-223 FAT FAT tumor suppressor (Drosophila) homolog miR-223, miR-125b, FGFR2 fibroblast growth factor receptor 2 miR-218 miR-92 FLI1 Friend leukemia virus integration 1 miR-24, miR-20 FLT1 fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor) miR-221 FOS v-fos FBJ murine osteosarcoma viral oncogene homolog miR-92 FOXG1B forkhead box G1B miR-223 FOXO3A forkhead box O3A miR-125b GOLGA5 golgi autoantigen, golgin subfamily a, 5 (PTC5) miR-138 GPHN gephyrin (GPH) miR-107, miR-223, HLF hepatic leukemia factor miR-20, miR-218 miR-26a, miR-107 HMGA1 high mobility group AT-hook 1 miR-20 HOXA13 homeo box A13 miR-92 HOXA9 homeo box A9 miR-125b IRF4 interferon regulatory factor 4 miR-146, miR-20, JAZF1 juxtaposed with another zinc finger gene 1 miR-138 miR-92 JUN v-jun avian sarcoma virus 17 oncogene homolog miR-155 KRAS v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog miR-218 LASP1 LIM and SH3 protein 1 miR-218 LHFP lipoma HMGIC fusion partner miR-125b, miR-218 LIFR leukemia inhibitory factor receptor miR-223 LMO2 LIM domain only 2 (rhombotin-like 1) (RBTN2) miR-223, miR-155, MAF v-maf musculoaponeurotic fibrosarcoma (avian) miR-125b, miR-92 oncogene homolog miR-92 MAP2K4 mitogen-activated protein kinase kinase 4 miR-146, miR-20 MAP3K8 mitogen-activated protein kinase kinase kinase 8 miR-125b MAX MAX protein miR-218 MCC mutated in colorectal cancers miR-24 MEN1 multiple endocrine neoplasia I miR-138 MLLT6 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila): translocated to, 6 (AF17) miR-192 MSN moesin miR-24 MYB v-myb avian myeloblastosis viral oncogene homolog miR-107, miR-223, MYBL1 v-myb avian myeloblastosis viral oncogene miR-146, miR-221, homolog-like 1 miR-155, miR-218 miR-107, miR-20 MYCN v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived miR-107, miR-92 MYH9 myosin. heavy polypeptide 9. non-muscle miR-24 MYST4 MYST histone acetyltransferase (monocytic leukemia) 4 (MORF) miR-20 NBL1 neuroblastoma, suppression of tumorigenicity 1 miR-125b NIN ninein (GSK3B interacting protein) miR-26a, miR-107 NKTR natural killer-tumor recognition sequence miR-92 NOTCH1 Notch homolog 1, translocation-associated (Drosophila) (TAN1) miR-24 NTRK3 neurotrophic tyrosine kinase, receptor, type 3 miR-125b PCSK7 proprotein convertase subtilisin/kexin type 7 miR-24, miR-146 PER1 period homolog 1 (Drosophila) miR-146, miR-125b, PHOX2B paired-like homeobox 2b miR-138, miR-155 PICALM phosphatidylinositol binding clathrin assembly protein (CALM) miR-24, miR-26a PIM1 pim-1 oncogene miR-24, miR-26a, PLAG1 pleiomorphic adenoma gene 1 miR-21, miR-107, miR-20, miR-155 miR-218 RAB8A RAB8A, member RAS oncogene family miR-24, miR-221 RALA v-ral simian leukemia viral oncogene homolog A (ras related) miR-138 RARA retinoic acid receptor, alpha miR-20, miR-192 RB1 retinoblastoma 1 (including osteosarcoma) miR-20, RBL1 retinoblastoma-like 1 (p107) miR-20 RBL2 retinoblastoma-like 2 (p130) miR-155, miR-138 REL v-rel avian reticuloendotheliosis viral oncogene homolog miR-20, miR-138 RHOC ras homolog gene family, member C miR-20, miR-192 RUNX1 runt-related transcription factor 1 (AML1) miR-107, miR-223 SEPT6 septin 6 miR-146, miR-20, SET SET translocation miR-125b miR-21, miR-20, SKI v-ski avian sarcoma viral oncogene homolog miR-155, miR-218 miR-26a, miR-146 SMAD4 SMAD, mothers against DPP homolog 4 (Drosophila) miR-155 SPI1 spleen focus forming virus (SFFV) proviral integration oncogene spi1 miR-125b SS18 synovial sarcoma translocation, chromosome 18 miR-107, miR-155 SUFU suppressor of fused homolog (Drosophila) miR-92 TAF15 TAF15 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68 kDa miR-26a, miR-221, TCF12 transcription factor 12 (HTF4, helix-loop-helix miR-138 transcription factors 4) miR-21, miR-20 TGFBR2 transforming growth factor, beta receptor II (70-80 kD) miR-24, miR-26a, TOP1 topoisomerase (DNA) I miR-92 miR-138 TPM4 tropomyosin 4 miR-20 TRIP11 thyroid hormone receptor interactor 11 miR-92 TSC1 Tuberous sclerosis 1 miR-20 TSG101 Tumor susceptibility gene 101 miR-20 TUSC2 Tumor suppressor candidate 2 miR-24 VAV1 vav 1 oncogene miR-125b VAV2 vav 2 oncogene miR-107 WHSC1 Wolf-Hirschhorn syndrome candidate 1(MMSET) miR-138 WHSC1L1 Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3) miR-26a WNT5A wingless-type MMTV integration site family, member 5A miR-26a, miR-20, YES1 v-yes-1 Yamaguchi sarcoma viral oncogene miR-125b homolog 1 miR-107, miR-221 ZNF198 zinc finger protein 198 miR-218 ZNFN1A1 zinc finger protein, subfamily 1A, 1 (Ikaros) *- Known cancer genes (e.g., tumor suppressors, oncogenes) comprise those identified in the Cancer Gene Census or reported by OMIM.

The relevant teachings of all publications cited herein that have not explicitly been incorporated by reference, are incorporated herein by reference in their entirety. While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims. 

What is claimed is:
 1. A method of diagnosing whether a subject has, or is at risk for developing, colon cancer, comprising: receiving a test sample of colon tissue extracted from a subject having, or suspected of having, colon cancer; measuring by Northern blot analysis the levels of miR-29b-2 gene product and at least one additional miR gene product in the test sample, wherein the at least one additional miR gene product comprises miR-21, and wherein the Northern blot analysis comprises: extracting nucleic acids from the test sample; treating the extracted nucleic acids with DNase to remove DNA; separating RNA molecules in the extracted nucleic acids by gel electrophoresis; hybridizing the separated RNA molecules to labeled probes; and detecting and quantifying the hybridization to determine the level of at least miR-29b-2 and miR-21 gene products; comparing the levels of the miR-29b-2 gene product and the at least one additional miR gene product in the test sample from the subject to the levels of corresponding gene products in a control sample of normal colon tissue; and diagnosing the subject as having, or being at risk for developing, colon cancer if the levels of miR-29b-2 gene product the at least one additional miR gene product in the test sample are higher than the levels of corresponding gene products in the control sample.
 2. A method of diagnosing whether a subject has, or is at risk for developing, colon cancer, comprising: receiving a test sample of colon tissue extracted from a subject having, or suspected of having, colon cancer; reverse transcribing at least two miR gene products from the test sample to provide at least two corresponding miR gene product target oligonucleotides; hybridizing at least two miR target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides that include at least two corresponding miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample, wherein the probe oligonucleotides are labeled with one of biotin, a radionuclide, a heavy metal, a fluorescent molecule, a chemiluminescent molecule, or an enzyme; comparing the test sample hybridization profile to a control hybridization profile for at least the two miR gene products in normal colon tissue; and diagnosing the subject as having, or being at risk for developing, colon cancer if the level of the at least two gene products in the test sample is greater than the control level of the two gene products, wherein the two miR gene products comprise miR-29b-2 and miR-21.
 3. The method of claim 2, wherein the probes are covalently attached to a polymeric matrix.
 4. The method of claim 2, wherein the miRNA-specific probe oligonucleotides comprise a sequence having at least about 70% complementarity to miR-29b-2.
 5. The method of claim 2, wherein the miRNA-specific probe oligonucleotides comprise a sequence having at least about 70% complementarity to miR-21.
 6. A method of diagnosing whether a subject has, or is at risk for developing, colon cancer, comprising: receiving a test sample of colon tissue extracted from a subject having, or suspected of having, colon cancer; reverse transcribing at least two miR gene products from the test sample to provide at least two corresponding miR gene product target oligonucleotides; hybridizing at least two miR target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides that include at least two corresponding miRNA-specific probe oligonucleotides covalently attached to a polymeric matrix, to provide a hybridization profile for the test sample; comparing the test sample hybridization profile to a control hybridization profile for the at least two miR gene products in normal colon tissue; and diagnosing the subject as having, or being at risk for developing, colon cancer if the level of the at least two gene products in the test sample is greater than the control level of the two gene products, wherein the two miR gene products comprise miR-29b-2 and miR-21. 